ProtoMol
- an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol File List
Here is a list of all files with brief descriptions:
AbstractEnumType.h
Angle.h
AngleInfo.cpp
AngleInfo.h
AngleSystemForce.h
AngleSystemForceBase.cpp
AngleSystemForceBase.h
Array.h
Array_Fastest.h
Array_NoPartialSpecialization.h
ArrayCellListStructure.cpp
ArrayCellListStructure.h
Atom.h
AtomType.h
BankLennardJonesParameterTable.h
BBKIntegrator.cpp
BBKIntegrator.h
Bond.h
BondSystemForce.h
BondSystemForceBase.cpp
BondSystemForceBase.h
BSpline.cpp
BSpline.h
BSplineMOLLYIntegrator.cpp
BSplineMOLLYIntegrator.h
BSplineType.cpp
BSplineType.h
buildCellLists.cpp
buildCellLists.h
buildISGTopology.cpp
buildISGTopology.h
buildTopology.cpp
buildTopology.h
C1SwitchingFunction.cpp
C1SwitchingFunction.h
C1SwitchingFunctionBase.cpp
C1SwitchingFunctionBase.h
C2SwitchingFunction.cpp
C2SwitchingFunction.h
C2SwitchingFunctionBase.cpp
C2SwitchingFunctionBase.h
CellListEnumerator.h
CellListEnumerator_periodicBoundaries.h
CellListEnumerator_standard.h
CompareForce.cpp
CompareForce.h
ComplementSwitchingFunction.h
ComplementSwitchingFunctionBase.cpp
ComplementSwitchingFunctionBase.h
Configuration.cpp
Configuration.h
ConfigurationReader.cpp
ConfigurationReader.h
ConstraintValueType.cpp
ConstraintValueType.h
coords2coords.cpp
coulomb.cpp
CoulombEwaldRealForce.cpp
CoulombEwaldRealForce.h
CoulombEwaldRealTableForce.cpp
CoulombEwaldRealTableForce.h
CoulombForce.cpp
CoulombForce.h
CoulombMultiGridDirectForce.h
CoulombMultiGridDirectForceBase.cpp
CoulombMultiGridDirectForceBase.h
CoulombMultiGridDirectTableForce.h
CoulombMultiGridDirectTableForceBase.cpp
CoulombMultiGridDirectTableForceBase.h
CubicCellLocation.h
CubicCellManager.cpp
CubicCellManager.h
CutoffSwitchingFunction.cpp
CutoffSwitchingFunction.h
CutoffSwitchingFunctionBase.cpp
CutoffSwitchingFunctionBase.h
Cycles.h
dcd2dcd.cpp
DCDTrajectoryReader.cpp
DCDTrajectoryReader.h
DCDTrajectoryWriter.cpp
DCDTrajectoryWriter.h
DihedralHMCIntegrator.cpp
DihedralHMCIntegrator.h
DihedralSystemForce.h
DihedralSystemForceBase.cpp
DihedralSystemForceBase.h
DLMCIntegrator.cpp
DLMCIntegrator.h
DMDLeapfrogIntegrator.cpp
DMDLeapfrogIntegrator.h
ElectricFieldSystemForce.h
ElectricFieldSystemForceBase.cpp
ElectricFieldSystemForceBase.h
EquilibriumMOLLYIntegrator.cpp
EquilibriumMOLLYIntegrator.h
ExclusionTable.cpp
ExclusionTable.h
ExclusionType.cpp
ExclusionType.h
ExtendedCompareForce.cpp
ExtendedCompareForce.h
ExtendedForce.cpp
ExtendedForce.h
ExtendedTimeForce.cpp
ExtendedTimeForce.h
ExternalGravitationSystemForce.cpp
ExternalGravitationSystemForce.h
ExternalMagneticFieldExtendedForce.cpp
ExternalMagneticFieldExtendedForce.h
Factory.h
fft.c
FFTComplex.cpp
FFTComplex.h
File.cpp
File.h
Force.cpp
Force.h
ForceFactory.h
ForceFactoryDetails.cpp
ForceFactoryDetails.h
ForceGroup.cpp
ForceGroup.h
FrictionExtendedForce.cpp
FrictionExtendedForce.h
GenericTopology.cpp
GenericTopology.h
GravitationForce.cpp
GravitationForce.h
Grid.h
HapticSystemForce.cpp
HapticSystemForce.h
HapticSystemForceBase.cpp
HapticSystemForceBase.h
HarmDihedralSystemForce.h
HarmDihedralSystemForceBase.cpp
HarmDihedralSystemForceBase.h
HelpTextFactory.cpp
HelpTextFactory.h
Hermite.cpp
Hermite.h
HMCIntegrator.cpp
HMCIntegrator.h
imd.cpp
imd.h
IMDElf.cpp
IMDElf.h
ImproperSystemForce.h
ImproperSystemForceBase.cpp
ImproperSystemForceBase.h
ImpulseIntegrator.cpp
ImpulseIntegrator.h
InputPosVel.cpp
InputPosVel.h
InputPosVelType.cpp
InputPosVelType.h
InputValue.h
inputValueDefinitions.cpp
inputValueDefinitions.h
Integrator.cpp
Integrator.h
IntegratorDefinition.cpp
IntegratorDefinition.h
IntegratorFactory.h
IntegratorFactoryDetails.cpp
IntegratorFactoryDetails.h
iSGAngleSystemForce.h
iSGAngleSystemForceBase.cpp
iSGAngleSystemForceBase.h
iSGBondSystemForce.h
iSGBondSystemForceBase.cpp
iSGBondSystemForceBase.h
iSGCoulombEwaldRealForce.cpp
iSGCoulombEwaldRealForce.h
iSGCoulombEwaldRealTableForce.cpp
iSGCoulombEwaldRealTableForce.h
iSGCoulombForce.cpp
iSGCoulombForce.h
iSGDihedralSystemForce.h
iSGDihedralSystemForceBase.cpp
iSGDihedralSystemForceBase.h
iSGGrid.h
iSGIdealGasCoulombForce.cpp
iSGIdealGasCoulombForce.h
iSGIdealGasLennardJonesForce.cpp
iSGIdealGasLennardJonesForce.h
iSGImproperSystemForce.h
iSGImproperSystemForceBase.cpp
iSGImproperSystemForceBase.h
iSGIntegrator.cpp
iSGIntegrator.h
iSGLennardJonesForce.cpp
iSGLennardJonesForce.h
iSGLennardJonesTableForce.cpp
iSGLennardJonesTableForce.h
iSGModifierPostForceChemostat.h
iSGModifierPreForceChemostat.h
iSGMTorsionSystemForce.h
iSGNonbondedFullEwaldSystemForce.h
iSGNonbondedFullEwaldSystemForceBase.cpp
iSGNonbondedFullEwaldSystemForceBase.h
iSGNonbondedPMEwaldSystemForce.h
iSGNonbondedPMEwaldSystemForceBase.cpp
iSGNonbondedPMEwaldSystemForceBase.h
iSGOneAtomPair.h
iSGOneAtomPairFull.h
iSGOneAtomPairTwo.h
iSGOneAtomPairTwoFull.h
iSGPAR.cpp
iSGPAR.h
iSGPARReader.cpp
iSGPARReader.h
iSGProtomol.cpp
iSGregisterForceExemplars.cpp
iSGregisterForceExemplars.h
iSGregisterForceExemplarsBonded.cpp
iSGregisterForceExemplarsBonded.h
iSGregisterForceExemplarsCutoff.cpp
iSGregisterForceExemplarsCutoff.h
iSGregisterForceExemplarsFastElectrostatic.cpp
iSGregisterForceExemplarsFastElectrostatic.h
iSGregisterForceExemplarsFull.cpp
iSGregisterForceExemplarsFull.h
iSGregisterForceExemplarsIdealGas.cpp
iSGregisterForceExemplarsIdealGas.h
iSGregisterForceExemplarsSimpleFull.cpp
iSGregisterForceExemplarsSimpleFull.h
iSGregisterIntegratorExemplars.cpp
iSGregisterIntegratorExemplars.h
iSGregisterOutputExemplars.cpp
iSGregisterOutputExemplars.h
Lagrange.cpp
Lagrange.h
LangevinImpulseIntegrator.cpp
LangevinImpulseIntegrator.h
LeapfrogIntegrator.cpp
LeapfrogIntegrator.h
LennardJonesForce.cpp
LennardJonesForce.h
LennardJonesParameters.h
LennardJonesParameterTable.cpp
LennardJonesParameterTable.h
LennardJonesTableForce.cpp
LennardJonesTableForce.h
MagneticDipoleForce.cpp
MagneticDipoleForce.h
MagneticDipoleMirrorSystemForce.h
MagneticDipoleMirrorSystemForceBase.cpp
MagneticDipoleMirrorSystemForceBase.h
Makeable.cpp
Makeable.h
MakeableDefinition.h
mathutilities.cpp
mathutilities.h
Matrix3by3.cpp
Matrix3by3.h
MCIntegrator.cpp
MCIntegrator.h
mdEnergy.cpp
MetaForce.cpp
MetaForce.h
Modifier.h
ModifierAveraging.h
ModifierFriction.h
ModifierIncrementTimestep.h
ModifierISG.cpp
ModifierISG.h
ModifierMetaRattle.cpp
ModifierMetaRattle.h
ModifierMetaRattleShake.cpp
ModifierMetaRattleShake.h
ModifierMetaShake.cpp
ModifierMetaShake.h
ModifierMollification.h
ModifierNPTRattle.cpp
ModifierNPTRattle.h
ModifierNPTShake.cpp
ModifierNPTShake.h
ModifierNVTRattle.cpp
ModifierNVTRattle.h
ModifierNVTShake.cpp
ModifierNVTShake.h
ModifierPostForceBarostat.h
ModifierPostForceThermostat.h
ModifierPreForceBarostat.h
ModifierPreForceThermostat.h
ModifierRattle.cpp
ModifierRattle.h
ModifierRemoveAngularMomentum.h
ModifierRemoveLinearMomentum.h
ModifierShake.cpp
ModifierShake.h
ModifierUpdateBeta.h
ModifierUpdateBetaAndPush.h
Molecule.h
MollyForce.cpp
MollyForce.h
MOLLYIntegrator.cpp
MOLLYIntegrator.h
MTorsionSystemForce.h
MTSIntegrator.cpp
MTSIntegrator.h
MultiGrid.h
NonbondedCutoffForce.h
NonbondedCutoffForceBase.cpp
NonbondedCutoffForceBase.h
NonbondedCutoffMollyForce.h
NonbondedCutoffSystemForce.h
NonbondedFullEwaldSystemForce.h
NonbondedFullEwaldSystemForceBase.cpp
NonbondedFullEwaldSystemForceBase.h
NonbondedFullSystemForce.h
NonbondedFullSystemForceBase.cpp
NonbondedFullSystemForceBase.h
NonbondedMultiGridSystemForce.h
NonbondedMultiGridSystemForceBase.cpp
NonbondedMultiGridSystemForceBase.h
NonbondedPMEwaldSystemForce.h
NonbondedPMEwaldSystemForceBase.cpp
NonbondedPMEwaldSystemForceBase.h
NonbondedSimpleFullSystemForce.h
NonbondedSimpleFullSystemForceBase.cpp
NonbondedSimpleFullSystemForceBase.h
NonStandardIntegrator.h
NoseNVTLeapfrogIntegrator.cpp
NoseNVTLeapfrogIntegrator.h
NPTVerletIntegrator.cpp
NPTVerletIntegrator.h
NVTVerletIntegrator.cpp
NVTVerletIntegrator.h
ObjectDefinition.h
oneAtomContraints.h
OneAtomPair.h
OneAtomPairFull.h
OneAtomPairTwo.h
OneAtomPairTwoFull.h
OneMollyPair.h
OneMollyPairTwo.h
openglutilities.cpp
openglutilities.h
Output.cpp
Output.h
OutputCache.cpp
OutputCache.h
OutputCollection.cpp
OutputCollection.h
OutputDCDTrajectory.cpp
OutputDCDTrajectory.h
OutputDiffusion.cpp
OutputDiffusion.h
OutputDihedrals.cpp
OutputDihedrals.h
OutputEnergies.cpp
OutputEnergies.h
OutputFactory.h
OutputFactoryDetails.cpp
OutputFactoryDetails.h
OutputFile.cpp
OutputFile.h
OutputFinalPDBPos.cpp
OutputFinalPDBPos.h
OutputFinalPSF.cpp
OutputFinalPSF.h
OutputFinalXSC.cpp
OutputFinalXSC.h
OutputFinalXYZBinPos.cpp
OutputFinalXYZBinPos.h
OutputFinalXYZBinVel.cpp
OutputFinalXYZBinVel.h
OutputFinalXYZPos.cpp
OutputFinalXYZPos.h
OutputFinalXYZVel.cpp
OutputFinalXYZVel.h
OutputISGProperties.cpp
OutputISGProperties.h
OutputMomentum.cpp
OutputMomentum.h
OutputPaulTrap.cpp
OutputPaulTrap.h
OutputPDBFramePos.cpp
OutputPDBFramePos.h
OutputScreen.cpp
OutputScreen.h
OutputTemperatures.cpp
OutputTemperatures.h
OutputXYZTrajectoryForce.cpp
OutputXYZTrajectoryForce.h
OutputXYZTrajectoryPos.cpp
OutputXYZTrajectoryPos.h
OutputXYZTrajectoryVel.cpp
OutputXYZTrajectoryVel.h
PAR.cpp
PAR.h
Parallel.cpp
Parallel.h
ParallelType.cpp
ParallelType.h
Parameter.cpp
Parameter.h
PARReader.cpp
PARReader.h
parseCommandLine.cpp
parseCommandLine.h
PARWriter.cpp
PARWriter.h
PaulTrapExtendedForce.h
PaulTrapExtendedForceBase.cpp
PaulTrapExtendedForceBase.h
PaulTrapIntegrator.cpp
PaulTrapIntegrator.h
PDB.cpp
PDB.h
PDBReader.cpp
PDBReader.h
PDBWriter.cpp
PDBWriter.h
PeriodicBoundaryConditions.cpp
PeriodicBoundaryConditions.h
PGM.cpp
PGM.h
PGMReader.cpp
PGMReader.h
PGMWriter.cpp
PGMWriter.h
PLeapfrogIntegrator.cpp
PLeapfrogIntegrator.h
pmconstants.cpp
pmconstants.h
PNGWriter.cpp
PNGWriter.h
PPM.cpp
PPM.h
PPMReader.cpp
PPMReader.h
PPMWriter.cpp
PPMWriter.h
protomol.cpp
protomol.h
Proxy.h
PSF.cpp
PSF.h
PSFReader.cpp
PSFReader.h
PSFWriter.cpp
PSFWriter.h
RangeSwitchingFunction.h
RangeSwitchingFunctionBase.cpp
RangeSwitchingFunctionBase.h
Reader.cpp
Reader.h
Real.h
ReducedHessAngle.cpp
ReducedHessAngle.h
reducedHessBond.cpp
reducedHessBond.h
ReducedHessCoulomb.cpp
ReducedHessCoulomb.h
ReducedHessLennardJones.cpp
ReducedHessLennardJones.h
ReducedHessTraits.h
framework/factories/registerForceExemplars.cpp
applications/coulomb-app/registerForceExemplars.cpp
framework/factories/registerForceExemplars.h
applications/coulomb-app/registerForceExemplars.h
registerForceExemplarsBonded.cpp
registerForceExemplarsBonded.h
registerForceExemplarsCutoff.cpp
registerForceExemplarsCutoff.h
registerForceExemplarsFastElectrostatic.cpp
registerForceExemplarsFastElectrostatic.h
registerForceExemplarsFull.cpp
registerForceExemplarsFull.h
registerForceExemplarsOther.cpp
registerForceExemplarsOther.h
registerForceExemplarsSimpleFull.cpp
registerForceExemplarsSimpleFull.h
framework/factories/registerIntegratorExemplars.cpp
applications/coulomb-app/registerIntegratorExemplars.cpp
framework/factories/registerIntegratorExemplars.h
applications/coulomb-app/registerIntegratorExemplars.h
framework/factories/registerOutputExemplars.cpp
applications/coulomb-app/registerOutputExemplars.cpp
framework/factories/registerOutputExemplars.h
applications/coulomb-app/registerOutputExemplars.h
framework/factories/registerTopologyExemplars.cpp
applications/coulomb-app/registerTopologyExemplars.cpp
framework/factories/registerTopologyExemplars.h
applications/coulomb-app/registerTopologyExemplars.h
Report.cpp
Report.h
ScalarStructure.cpp
ScalarStructure.h
SemiGenericTopology.h
ShadowHMCIntegrator.cpp
ShadowHMCIntegrator.h
ShiftSwitchingFunction.cpp
ShiftSwitchingFunction.h
ShiftSwitchingFunctionBase.cpp
ShiftSwitchingFunctionBase.h
simpleTypes.h
SphericalSystemForce.cpp
SphericalSystemForce.h
sstream_local.h
Stack.h
StandardIntegrator.cpp
StandardIntegrator.h
stringutilities.cpp
stringutilities.h
STSIntegrator.cpp
STSIntegrator.h
SystemCompareForce.cpp
SystemCompareForce.h
SystemForce.cpp
SystemForce.h
SystemTimeForce.cpp
SystemTimeForce.h
systemutilities.cpp
systemutilities.h
TimeForce.cpp
TimeForce.h
Timer.cpp
Timer.h
TimerStatistic.cpp
TimerStatistic.h
Topology.h
TopologyFactory.h
TopologyFactoryDetails.cpp
TopologyFactoryDetails.h
topologyutilities.cpp
topologyutilities.h
Torsion.h
TRANS.cpp
TRANS.h
TRANSReader.cpp
TRANSReader.h
typeSelection.h
UmbrellaIntegrator.cpp
UmbrellaIntegrator.h
UniversalSwitchingFunction.h
UniversalSwitchingFunctionBase.cpp
UniversalSwitchingFunctionBase.h
VacuumBoundaryConditions.cpp
VacuumBoundaryConditions.h
Value.cpp
Value.h
ValueType.cpp
ValueType.h
Vector.h
Vector3D.h
Vector3DBlock.cpp
Vector3DBlock.h
vmdsock.cpp
vmdsock.h
WrapperMetaForce.cpp
WrapperMetaForce.h
Writer.cpp
Writer.h
XFigWriter.cpp
XFigWriter.h
XSC.cpp
XSC.h
XSCReader.cpp
XSCReader.h
XSCWriter.cpp
XSCWriter.h
XYZ.cpp
XYZ.h
XYZBinReader.cpp
XYZBinReader.h
XYZBinWriter.cpp
XYZBinWriter.h
XYZReader.cpp
XYZReader.h
XYZTrajectoryReader.cpp
XYZTrajectoryReader.h
XYZTrajectoryWriter.cpp
XYZTrajectoryWriter.h
xyzviz.cpp
XYZWriter.cpp
XYZWriter.h
Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.
