Index

A

AllInfo (built-in class) AllInfo.addAngleType() built-in function AllInfo.addAngleTypeByPairs() built-in function AllInfo.addBondType() built-in function AllInfo.addBondTypeByPairs() built-in function AllInfo.addParticleType() built-in function AllInfo.setNDimensions() built-in function AndersenNVT (built-in class) AndersenNVT.setT() built-in function, [1] AngleForceCos (built-in class) AngleForceCos.setParams() built-in function AngleForceHarmonic (built-in class), [1] AngleForceHarmonic.setParams() built-in function AngleForceHarmonicCos (built-in class), [1] AngleForceHarmonicCos.setParams() built-in function AngleForceLnExp (built-in class) AngleForceLnExp.setParams() built-in function AngleForceTable (built-in class)

AngleForceTable.setParams() built-in function AngleForceTable.setPotential() built-in function, [1] AniForce (built-in class) AniForce.setParams() built-in function AniForce.setPatches() built-in function Application (built-in class) Application.add() built-in function Application.clear() built-in function application.dynamics (built-in class) application.dynamics.add() built-in function application.dynamics.remove() built-in function application.dynamics.run() built-in function Application.remove() built-in function Application.run() built-in function Application.setDt() built-in function AxialStretching (built-in class) AxialStretching.setBoxLength() built-in function

B

BerendsenAniNVT (built-in class) BerendsenAniNVT.setT() built-in function, [1] BerendsenAniNVT.setTau() built-in function BerendsenNVT (built-in class) BerendsenNVT.setT() built-in function, [1] BinaryDump (built-in class) BinaryDump.enableCompression() built-in function BinaryDump.setOutput() built-in function BinaryDump.setOutputAll() built-in function BinaryDump.setOutputForRestart() built-in function BinaryReader (built-in class) BondConstraint (built-in class), [1] BondConstraint.setExpansionOrder() built-in function, [1] BondConstraint.setNumIters() built-in function, [1] BondConstraint.setParams() built-in function BondForceAni (built-in class) BondForceAni.setParams() built-in function BondForceFENE (built-in class) BondForceFENE.setConsiderDiameter() built-in function BondForceFENE.setParams() built-in function, [1], [2] BondForceHarmonic (built-in class), [1] BondForceHarmonic.setParams() built-in function BondForceMorse (built-in class) BondForceMorse.setParams() built-in function BondForcePolynomial (built-in class) BondForcePolynomial.setParams() built-in function BondForceTable (built-in class) BondForceTable.setParams() built-in function BondForceTable.setPotential() built-in function, [1] BounceBackConstrain (built-in class) BounceBackConstrain.addCylinder() built-in function BounceBackConstrain.addSphere() built-in function BounceBackConstrain.addWall() built-in function BounceBackConstrain.clcearWall() built-in function BounceBackConstrain.clearCylinder() built-in function BounceBackConstrain.clearSphere() built-in function built-in function AllInfo.addAngleType() AllInfo.addAngleTypeByPairs() AllInfo.addBondType() AllInfo.addBondTypeByPairs() AllInfo.addParticleType() AllInfo.setNDimensions() AndersenNVT.setT(), [1] AngleForceCos.setParams() AngleForceHarmonic.setParams() AngleForceHarmonicCos.setParams() AngleForceLnExp.setParams() AngleForceTable.setParams() AngleForceTable.setPotential(), [1] AniForce.setParams() AniForce.setPatches() Application.add() Application.clear() application.dynamics.add() application.dynamics.remove() application.dynamics.run() Application.remove() Application.run() Application.setDt() AxialStretching.setBoxLength() BerendsenAniNVT.setT(), [1] BerendsenAniNVT.setTau() BerendsenNVT.setT(), [1] BinaryDump.enableCompression() BinaryDump.setOutput() BinaryDump.setOutputAll() BinaryDump.setOutputForRestart() BondConstraint.setExpansionOrder(), [1] BondConstraint.setNumIters(), [1] BondConstraint.setParams() BondForceAni.setParams() BondForceFENE.setConsiderDiameter() BondForceFENE.setParams(), [1], [2] BondForceHarmonic.setParams() BondForceMorse.setParams() BondForcePolynomial.setParams() BondForceTable.setParams() BondForceTable.setPotential(), [1] BounceBackConstrain.addCylinder() BounceBackConstrain.addSphere() BounceBackConstrain.addWall() BounceBackConstrain.clcearWall() BounceBackConstrain.clearCylinder() BounceBackConstrain.clearSphere() CCPMD.setParams() CCPMD.setWall() CellList.setDataReproducibility() CellList.setNominalDim() CellList.setNominalWidth() CenterForce.setPreNextShift() ChangeType.setInterface() ChangeType.setNPTargetType() ChangeType.setPr() ChangeType.setSite() ChangeType.setWall() ComputeInfo.setNdof() DCDDump.unpbc() DCDDump.unwrap() DePolymerization.setParams() DePolymerization.setT(), [1] DihedralForceAmberCosine.setParams() DihedralForceHarmonic.setCosFactor() DihedralForceHarmonic.setParams(), [1], [2] DihedralForceOPLSCosine.setParams(), [1] DihedralForceRyckaertBellemans.setParams() DihedralForceTable.setParams() DihedralForceTable.setPotential(), [1] DPDEwaldForce.setBeta() DPDEwaldForce.setParams(), [1] DPDForce.setDPDVV() DPDForce.setParams() DPDForce.setT(), [1] DPDGWVV.setLambda() DumpInfo.dumpAnisotropy() DumpInfo.dumpBoxSize() DumpInfo.dumpParticleForce() DumpInfo.dumpParticlePosition() DumpInfo.dumpPotential() DumpInfo.dumpPressTensor() DumpInfo.dumpTypeTemp() DumpInfo.dumpVirial() DumpInfo.dumpVirialMatrix() DumpInfo.setPeriod() ENUFForce.setParams() EwaldForce.setParams(), [1] ExternalForce.setForce(), [1] ExternalForce.setParams(), [1] force.angle.setParams() force.bond.setParams() force.dihedral.setCosFactor() force.dihedral.setParams() force.dpd.setParams() force.nonbonded.setParams() force.nonbonded_c.setParams() GBForce.setParams() GEMForce.setParams(), [1] Generators.addMolecule() Generators.outPutMol2() Generators.outPutMST() Generators.outPutXML() Generators.setDimension() Generators.setMinimumDistance(), [1] Generators.setParam() integration.bd.setParams() integration.nvt.setT(), [1] LangevinNVT.setGamma(), [1] LangevinNVT.setT(), [1] LangevinNVTRigid.setGamma(), [1] LangevinNVTRigid.setT(), [1] LJConstrainForce.addCylinder() LJConstrainForce.addSphere() LJConstrainForce.addWall() LJConstrainForce.clcearWall() LJConstrainForce.clearCylinder() LJConstrainForce.clearSphere() LJConstrainForce.setParams() LJEwaldForce.setDispVirialCorr(), [1] LJEwaldForce.setEnergy_shift(), [1] LJEwaldForce.setParams(), [1] LJForce.setDispVirialCorr() LJForce.setEnergy_shift() LJForce.setParams(), [1] LZWForce.setMethod() LZWForce.setParams() MDSCFForce.setNewVersion() MDSCFForce.setParams() MDSCFForce.setPeriodScf() MOL2Dump.deleteBoundaryBond() MOL2Dump.setChangeFreeType() Molecule.setAngleDegree(), [1] Molecule.setBody(), [1], [2] Molecule.setBodyEvacuation() Molecule.setBondLength(), [1] Molecule.setBox(), [1] Molecule.setCharge(), [1], [2] Molecule.setCris(), [1], [2] Molecule.setCylinder() Molecule.setDiameter(), [1], [2] Molecule.setDihedralDegree(), [1] Molecule.setInert(), [1], [2] Molecule.setInit(), [1], [2] Molecule.setIsotactic() Molecule.setMass(), [1], [2] Molecule.setMolecule(), [1], [2] Molecule.setOrientation(), [1], [2] Molecule.setParticleTypes() Molecule.setQuaternion(), [1], [2] Molecule.setSphere() Molecule.setTopology() NeighborList.addExclusionsFromAngles() NeighborList.addExclusionsFromBodies() NeighborList.addExclusionsFromBonds() NeighborList.addExclusionsFromDihedrals() NeighborList.setDataReproducibility() NeighborList.setFilterDiameters() NeighborList.setNsq() NeighborList.setRCut() NeighborList.setRCutPair() NoseHooverNVT.setT(), [1] NPT.setP() NPT.setT(), [1] NPTMTK.setAnisotropic() NPTMTK.setSemiisotropic(), [1] NPTMTK.setT(), [1] NPTMTKRigid.setAnisotropic() NPTMTKRigid.setSemiisotropic(), [1] NPTMTKRigid.setT(), [1] NPTRigid.setP() NPTRigid.setT(), [1] NVE.setZeroForce() NVTRigid.setT(), [1] Object.setRadius() PairForce.setParams() PairForce.setShiftParams() PairForceTable.setParams() PairForceTable.setPotential(), [1] ParticleSet.getNumMembers() PBGBForce.setAspheres() PBGBForce.setGUM() PBGBForce.setParams() PBGBForce.setPatches() PFMEForce.setNewVersion() PFMEForce.setPeriodPFME() Polymerization.generateAngle() Polymerization.generateDihedral() Polymerization.initExPoint() Polymerization.setEnergyBar() Polymerization.setExchangePr() Polymerization.setExchMode() Polymerization.setFrpMode() Polymerization.setFuncReactRule() Polymerization.setMaxCris() Polymerization.setMinDisReactRule() Polymerization.setNewAngleType() Polymerization.setNewAngleTypeByPairs() Polymerization.setNewBondType() Polymerization.setNewBondTypeByPairs() Polymerization.setNewDihedralType() Polymerization.setPr(), [1] Polymerization.setPrFactor(), [1] Polymerization.setSgapMode() PPPMForce.setParams(), [1] RNEMD.setPeriod() RNEMD.setProfVelPeriod() RNEMD.setSwapGroup() RNEMD.setSwapPeriod() RNEMD.setVelProfile() setHead() setPrecision() SLJForce.setEnergy_shift() SLJForce.setParams(), [1] TranRigid.setRotDimension() TranRigid.setTraDimension() VariantLinear.setPoint() VariantSin.setPoint() VariantWell.setPoint() Vsite.setParams() XMLDump.setOutput() XMLDump.setOutputAngle() XMLDump.setOutputBody() XMLDump.setOutputBond() XMLDump.setOutputCharge() XMLDump.setOutputConstraint() XMLDump.setOutputCris() XMLDump.setOutputDiameter() XMLDump.setOutputDihedral() XMLDump.setOutputEllipsoid(), [1], [2] XMLDump.setOutputForce() XMLDump.setOutputImage() XMLDump.setOutputInert() XMLDump.setOutputInit() XMLDump.setOutputLocalForce() XMLDump.setOutputLocalVirial() XMLDump.setOutputLocalVirialMatrix() XMLDump.setOutputMass() XMLDump.setOutputOrientation() XMLDump.setOutputPatch() XMLDump.setOutputPosition() XMLDump.setOutputPotential() XMLDump.setOutputQuaternion() XMLDump.setOutputRotangle() XMLDump.setOutputRotation() XMLDump.setOutputTorque() XMLDump.setOutputType() XMLDump.setOutputVelocity() XMLDump.setOutputVirial() XMLDump.setOutputVsite()

C

CCPMD (built-in class) CCPMD.setParams() built-in function CCPMD.setWall() built-in function CellList (built-in class) CellList.setDataReproducibility() built-in function CellList.setNominalDim() built-in function CellList.setNominalWidth() built-in function CenterForce (built-in class) CenterForce.setPreNextShift() built-in function

ChangeType (built-in class) ChangeType.setInterface() built-in function ChangeType.setNPTargetType() built-in function ChangeType.setPr() built-in function ChangeType.setSite() built-in function ChangeType.setWall() built-in function chare.particle_set (built-in class) ComputeInfo (built-in class) ComputeInfo.setNdof() built-in function

D

DCDDump (built-in class), [1] DCDDump.unpbc() built-in function DCDDump.unwrap() built-in function DePolymerization (built-in class) DePolymerization.setParams() built-in function DePolymerization.setT() built-in function, [1] DihedralForceAmberCosine (built-in class), [1] DihedralForceAmberCosine.setParams() built-in function DihedralForceHarmonic (built-in class), [1], [2] DihedralForceHarmonic.setCosFactor() built-in function DihedralForceHarmonic.setParams() built-in function, [1], [2] DihedralForceOPLSCosine (built-in class) DihedralForceOPLSCosine.setParams() built-in function, [1] DihedralForceRyckaertBellemans (built-in class) DihedralForceRyckaertBellemans.setParams() built-in function DihedralForceTable (built-in class) DihedralForceTable.setParams() built-in function DihedralForceTable.setPotential() built-in function, [1] DPDEwaldForce (built-in class) DPDEwaldForce.setBeta() built-in function DPDEwaldForce.setParams() built-in function, [1]

DPDForce (built-in class), [1] DPDForce.setDPDVV() built-in function DPDForce.setParams() built-in function DPDForce.setT() built-in function, [1] DPDGWVV (built-in class) DPDGWVV.setLambda() built-in function dump.data (built-in class) dump.mst (built-in class) dump.xml (built-in class) DumpInfo (built-in class) DumpInfo.dumpAnisotropy() built-in function DumpInfo.dumpBoxSize() built-in function DumpInfo.dumpParticleForce() built-in function DumpInfo.dumpParticlePosition() built-in function DumpInfo.dumpPotential() built-in function DumpInfo.dumpPressTensor() built-in function DumpInfo.dumpTypeTemp() built-in function DumpInfo.dumpVirial() built-in function DumpInfo.dumpVirialMatrix() built-in function DumpInfo.setPeriod() built-in function

E

ENUFForce (built-in class) ENUFForce.setParams() built-in function EwaldForce (built-in class) EwaldForce.setParams() built-in function, [1]

ExternalForce (built-in class) ExternalForce.setForce() built-in function, [1] ExternalForce.setParams() built-in function, [1]

F

force.angle (built-in class) force.angle.setParams() built-in function force.bond (built-in class) force.bond.setParams() built-in function force.dihedral (built-in class) force.dihedral.setCosFactor() built-in function force.dihedral.setParams() built-in function

force.dpd (built-in class) force.dpd.setParams() built-in function force.nonbonded (built-in class) force.nonbonded.setParams() built-in function force.nonbonded_c (built-in class) force.nonbonded_c.setParams() built-in function

G

GBForce (built-in class) GBForce.setParams() built-in function GEMForce (built-in class) GEMForce.setParams() built-in function, [1] Generators (built-in class) Generators.addMolecule() built-in function Generators.outPutMol2() built-in function

Generators.outPutMST() built-in function Generators.outPutXML() built-in function Generators.setDimension() built-in function Generators.setMinimumDistance() built-in function, [1] Generators.setParam() built-in function

I

integration.bd (built-in class) integration.bd.setParams() built-in function

integration.gwvv (built-in class), [1] integration.nvt (built-in class) integration.nvt.setT() built-in function, [1]

L

LangevinNVT (built-in class) LangevinNVT.setGamma() built-in function, [1] LangevinNVT.setT() built-in function, [1] LangevinNVTRigid (built-in class) LangevinNVTRigid.setGamma() built-in function, [1] LangevinNVTRigid.setT() built-in function, [1] LJConstrainForce (built-in class) LJConstrainForce.addCylinder() built-in function LJConstrainForce.addSphere() built-in function LJConstrainForce.addWall() built-in function LJConstrainForce.clcearWall() built-in function LJConstrainForce.clearCylinder() built-in function LJConstrainForce.clearSphere() built-in function

LJConstrainForce.setParams() built-in function LJCoulombShiftForce (built-in class) LJEwaldForce (built-in class), [1] LJEwaldForce.setDispVirialCorr() built-in function, [1] LJEwaldForce.setEnergy_shift() built-in function, [1] LJEwaldForce.setParams() built-in function, [1] LJForce (built-in class) LJForce.setDispVirialCorr() built-in function LJForce.setEnergy_shift() built-in function LJForce.setParams() built-in function, [1] LZWForce (built-in class) LZWForce.setMethod() built-in function LZWForce.setParams() built-in function

M

MDSCFForce (built-in class) MDSCFForce.setNewVersion() built-in function MDSCFForce.setParams() built-in function MDSCFForce.setPeriodScf() built-in function MOL2Dump (built-in class) MOL2Dump.deleteBoundaryBond() built-in function MOL2Dump.setChangeFreeType() built-in function Molecule (built-in class), [1] Molecule.setAngleDegree() built-in function, [1] Molecule.setBody() built-in function, [1], [2] Molecule.setBodyEvacuation() built-in function Molecule.setBondLength() built-in function, [1] Molecule.setBox() built-in function, [1] Molecule.setCharge() built-in function, [1], [2] Molecule.setCris() built-in function, [1], [2]

Molecule.setCylinder() built-in function Molecule.setDiameter() built-in function, [1], [2] Molecule.setDihedralDegree() built-in function, [1] Molecule.setInert() built-in function, [1], [2] Molecule.setInit() built-in function, [1], [2] Molecule.setIsotactic() built-in function Molecule.setMass() built-in function, [1], [2] Molecule.setMolecule() built-in function, [1], [2] Molecule.setOrientation() built-in function, [1], [2] Molecule.setParticleTypes() built-in function Molecule.setQuaternion() built-in function, [1], [2] Molecule.setSphere() built-in function Molecule.setTopology() built-in function

N

NeighborList (built-in class) NeighborList.addExclusionsFromAngles() built-in function NeighborList.addExclusionsFromBodies() built-in function NeighborList.addExclusionsFromBonds() built-in function NeighborList.addExclusionsFromDihedrals() built-in function NeighborList.setDataReproducibility() built-in function NeighborList.setFilterDiameters() built-in function NeighborList.setNsq() built-in function NeighborList.setRCut() built-in function NeighborList.setRCutPair() built-in function NoseHooverNVT (built-in class) NoseHooverNVT.setT() built-in function, [1] NPT (built-in class) NPT.setP() built-in function NPT.setT() built-in function, [1]

NPTMTK (built-in class) NPTMTK.setAnisotropic() built-in function NPTMTK.setSemiisotropic() built-in function, [1] NPTMTK.setT() built-in function, [1] NPTMTKRigid (built-in class) NPTMTKRigid.setAnisotropic() built-in function NPTMTKRigid.setSemiisotropic() built-in function, [1] NPTMTKRigid.setT() built-in function, [1] NPTRigid (built-in class) NPTRigid.setP() built-in function NPTRigid.setT() built-in function, [1] NVE (built-in class) NVE.setZeroForce() built-in function NVERigid (built-in class) NVTRigid (built-in class) NVTRigid.setT() built-in function, [1]

O

Object (built-in class), [1]

Object.setRadius() built-in function

P

PairForce (built-in class) PairForce.setParams() built-in function PairForce.setShiftParams() built-in function PairForceTable (built-in class) PairForceTable.setParams() built-in function PairForceTable.setPotential() built-in function, [1] ParticleSet (built-in class), [1], [2], [3] ParticleSet.getNumMembers() built-in function PBGBForce (built-in class) PBGBForce.setAspheres() built-in function PBGBForce.setGUM() built-in function PBGBForce.setParams() built-in function PBGBForce.setPatches() built-in function PerformConfig (built-in class) PFMEForce (built-in class) PFMEForce.setNewVersion() built-in function PFMEForce.setPeriodPFME() built-in function Polymerization (built-in class), [1] Polymerization.generateAngle() built-in function Polymerization.generateDihedral() built-in function Polymerization.initExPoint() built-in function

Polymerization.setEnergyBar() built-in function Polymerization.setExchangePr() built-in function Polymerization.setExchMode() built-in function Polymerization.setFrpMode() built-in function Polymerization.setFuncReactRule() built-in function Polymerization.setMaxCris() built-in function Polymerization.setMinDisReactRule() built-in function Polymerization.setNewAngleType() built-in function Polymerization.setNewAngleTypeByPairs() built-in function Polymerization.setNewBondType() built-in function Polymerization.setNewBondTypeByPairs() built-in function Polymerization.setNewDihedralType() built-in function Polymerization.setPr() built-in function, [1] Polymerization.setPrFactor() built-in function, [1] Polymerization.setSgapMode() built-in function PPPMForce (built-in class) PPPMForce.setParams() built-in function, [1]

R

Reader (built-in class) RNEMD (built-in class) RNEMD.setPeriod() built-in function RNEMD.setProfVelPeriod() built-in function

RNEMD.setSwapGroup() built-in function RNEMD.setSwapPeriod() built-in function RNEMD.setVelProfile() built-in function

S

setHead() built-in function setPrecision() built-in function SLJForce (built-in class) SLJForce.setEnergy_shift() built-in function

SLJForce.setParams() built-in function, [1] snapshot (built-in class) snapshot.read (built-in class) Sort (built-in class)

T

TranRigid (built-in class) TranRigid.setRotDimension() built-in function

TranRigid.setTraDimension() built-in function

V

VariantConst (built-in class) VariantLinear (built-in class) VariantLinear.setPoint() built-in function VariantSin (built-in class) VariantSin.setPoint() built-in function

VariantWell (built-in class) VariantWell.setPoint() built-in function Vsite (built-in class), [1] Vsite.setParams() built-in function

X

XMLDump (built-in class), [1] XMLDump.setOutput() built-in function XMLDump.setOutputAngle() built-in function XMLDump.setOutputBody() built-in function XMLDump.setOutputBond() built-in function XMLDump.setOutputCharge() built-in function XMLDump.setOutputConstraint() built-in function XMLDump.setOutputCris() built-in function XMLDump.setOutputDiameter() built-in function XMLDump.setOutputDihedral() built-in function XMLDump.setOutputEllipsoid() built-in function, [1], [2] XMLDump.setOutputForce() built-in function XMLDump.setOutputImage() built-in function XMLDump.setOutputInert() built-in function XMLDump.setOutputInit() built-in function XMLDump.setOutputLocalForce() built-in function

XMLDump.setOutputLocalVirial() built-in function XMLDump.setOutputLocalVirialMatrix() built-in function XMLDump.setOutputMass() built-in function XMLDump.setOutputOrientation() built-in function XMLDump.setOutputPatch() built-in function XMLDump.setOutputPosition() built-in function XMLDump.setOutputPotential() built-in function XMLDump.setOutputQuaternion() built-in function XMLDump.setOutputRotangle() built-in function XMLDump.setOutputRotation() built-in function XMLDump.setOutputTorque() built-in function XMLDump.setOutputType() built-in function XMLDump.setOutputVelocity() built-in function XMLDump.setOutputVirial() built-in function XMLDump.setOutputVsite() built-in function XMLReader (built-in class)

Z

ZeroMomentum (built-in class), [1]