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C
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D
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E
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F
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G
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H
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I
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X
A
AdiabaticDynamicsIntegrator (class in atomsmm.integrators)
AlchemicalRespaSystem (class in atomsmm.systems)
AlchemicalSystem (class in atomsmm.systems)
atomsmm.computers (module)
atomsmm.forces (module)
atomsmm.integrators (module)
atomsmm.propagators (module)
atomsmm.reporters (module)
atomsmm.systems (module)
atomsmm.utils (module)
C
CenterOfMassReporter (class in atomsmm.reporters)
ChainedPropagator (class in atomsmm.propagators)
computers (module)
ComputingSystem (class in atomsmm.systems)
countDegreesOfFreedom() (in module atomsmm.utils)
CustomIntegratorReporter (class in atomsmm.reporters)
D
DampedSmoothedForce (class in atomsmm.forces)
E
evaluateForce() (in module atomsmm.utils)
ExpandedEnsembleReporter (class in atomsmm.reporters)
ExtendedStateDataReporter (class in atomsmm.reporters)
ExtendedSystemPropagator (class in atomsmm.propagators)
ExtendedSystemVariable (class in atomsmm.integrators)
F
FarNonbondedForce (class in atomsmm.forces)
findNonbondedForce() (in module atomsmm.utils)
forces (module)
G
GenericBoostPropagator (class in atomsmm.propagators)
GenericScalingPropagator (class in atomsmm.propagators)
get_atomic_pressure() (atomsmm.computers.PressureComputer method)
get_atomic_virial() (atomsmm.computers.PressureComputer method)
get_bond_virial() (atomsmm.computers.PressureComputer method)
get_coulomb_virial() (atomsmm.computers.PressureComputer method)
get_dispersion_virial() (atomsmm.computers.PressureComputer method)
get_molecular_pressure() (atomsmm.computers.PressureComputer method)
get_molecular_virial() (atomsmm.computers.PressureComputer method)
GlobalThermostatIntegrator (class in atomsmm.integrators)
H
hijackForce() (in module atomsmm.utils)
I
initialize() (atomsmm.integrators.AdiabaticDynamicsIntegrator method)
(atomsmm.integrators.LimitedSpeedBAOABIntegrator method)
(atomsmm.integrators.LimitedSpeedNHLIntegrator method)
(atomsmm.integrators.LimitedSpeedStochasticIntegrator method)
(atomsmm.integrators.LimitedSpeedStochasticVelocityIntegrator method)
(atomsmm.integrators.NewMethodIntegrator method)
(atomsmm.integrators.NHL_R_Integrator method)
(atomsmm.integrators.SIN_R_Integrator method)
InputError
integrator() (atomsmm.propagators.Propagator method)
integrators (module)
L
Langevin_R_Integrator (class in atomsmm.integrators)
LimitedSpeedBAOABIntegrator (class in atomsmm.integrators)
LimitedSpeedLangevinPropagator (class in atomsmm.propagators)
LimitedSpeedNHLIntegrator (class in atomsmm.integrators)
LimitedSpeedNHLPropagator (class in atomsmm.propagators)
LimitedSpeedStochasticIntegrator (class in atomsmm.integrators)
LimitedSpeedStochasticPropagator (class in atomsmm.propagators)
LimitedSpeedStochasticVelocityIntegrator (class in atomsmm.integrators)
LimitedSpeedStochasticVelocityPropagator (class in atomsmm.propagators)
M
MassiveGeneralizedGaussianMomentPropagator (class in atomsmm.propagators)
MassiveIsokineticPropagator (class in atomsmm.propagators)
MassiveNoseHooverPropagator (class in atomsmm.propagators)
MultipleTimeScaleIntegrator (class in atomsmm.integrators)
MultipleTimeScalePropagator (class in atomsmm.propagators)
N
NearExceptionForce (class in atomsmm.forces)
NearNonbondedForce (class in atomsmm.forces)
NewMethodIntegrator (class in atomsmm.integrators)
NewMethodPropagator (class in atomsmm.propagators)
NHL_R_Integrator (class in atomsmm.integrators)
NonbondedExceptionsForce (class in atomsmm.forces)
NoseHooverChainPropagator (class in atomsmm.propagators)
NoseHooverLangevinPropagator (class in atomsmm.propagators)
NoseHooverPropagator (class in atomsmm.propagators)
O
ODE
OrnsteinUhlenbeckPropagator (class in atomsmm.propagators)
P
PressureComputer (class in atomsmm.computers)
Propagator (class in atomsmm.propagators)
propagators (module)
R
redefine_angle() (atomsmm.systems.RESPASystem method)
redefine_bond() (atomsmm.systems.RESPASystem method)
RegulatedAtomicNoseHooverLangevinPropagator (class in atomsmm.propagators)
RegulatedBoostPropagator (class in atomsmm.propagators)
RegulatedMassiveNoseHooverLangevinPropagator (class in atomsmm.propagators)
RegulatedTranslationPropagator (class in atomsmm.propagators)
reporters (module)
reset_coulomb_scaling_factor() (atomsmm.systems.AlchemicalRespaSystem method)
RespaPropagator (class in atomsmm.propagators)
RESPASystem (class in atomsmm.systems)
RestrainedLangevinPropagator (class in atomsmm.propagators)
S
SDE
SIN_R_Integrator (class in atomsmm.integrators)
SIN_R_Propagator (class in atomsmm.propagators)
SoftcoreForce (class in atomsmm.forces)
SoftcoreLennardJonesForce (class in atomsmm.forces)
SolvationSystem (class in atomsmm.systems)
splitPotentialEnergy() (in module atomsmm.utils)
SplitPropagator (class in atomsmm.propagators)
state_sampling_analysis() (atomsmm.reporters.ExpandedEnsembleReporter method)
SuzukiYoshidaPropagator (class in atomsmm.propagators)
system (module)
T
TranslationPropagator (class in atomsmm.propagators)
TrotterSuzukiPropagator (class in atomsmm.propagators)
TwiceRegulatedAtomicNoseHooverLangevinPropagator (class in atomsmm.propagators)
TwiceRegulatedGlobalNoseHooverLangevinPropagator (class in atomsmm.propagators)
TwiceRegulatedMassiveNoseHooverLangevinPropagator (class in atomsmm.propagators)
U
UnconstrainedVelocityVerletPropagator (class in atomsmm.propagators)
utils (module)
V
VelocityBoostPropagator (class in atomsmm.propagators)
VelocityRescalingPropagator (class in atomsmm.propagators)
VelocityVerletPropagator (class in atomsmm.propagators)
X
XYZReporter (class in atomsmm.reporters)
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