Here is a list of all class members with links to the classes they belong to:
- o -
- O
: PLMD::isdb::SAXS
- obs_cvs_
: PLMD::opes::OPESexpanded
- obs_steps_
: PLMD::opes::OPESexpanded
- observable_freq_
: PLMD::fisst::FISST
- observable_weight_
: PLMD::fisst::FISST
- Oc
: PLMD::isdb::CS2Backbone
- occupancies
: PLMD::molfile::molfile_qm_wavefunction_t
- occupancy
: PLMD::generic::DumpPDB
, PLMD::molfile::molfile_atom_t
, PLMD::PDB
- of
: PLMD::generic::DumpAtoms
, PLMD::generic::DumpDerivatives
, PLMD::generic::DumpForces
, PLMD::generic::DumpProjections
- offset
: PLMD::bias::LWalls
, PLMD::bias::UWalls
- offset_
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- offset_c_
: PLMD::s2cm::S2ContactModel
- offset_max_
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- offset_min_
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- offset_mu_
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- offset_prior_
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- ofile
: PLMD::generic::Committor
, PLMD::generic::Debug
, PLMD::generic::Print
, PLMD::generic::PrintNDX
- OFile()
: PLMD::OFile
- old_KDEnorm_
: PLMD::opes::OPESmetad< mode >
- oldaa
: PLMD::bias::MovingRestraint
- olddpotdk
: PLMD::bias::MovingRestraint
- oldf
: PLMD::bias::MovingRestraint
- oldk
: PLMD::bias::MovingRestraint
- oldlambda
: PLMD::bias::MaxEnt
- on
: PLMD::DomainDecomposition::DomainComms
, PLMD::generic::UpdateIf
- one_minus_weight_decay_
: PLMD::ves::Opt_Adam
- onebead
: PLMD::isdb::SAXS
- oneD_pmf
: PLMD::drr::UIestimator::UIestimator
- onefile
: PLMD::generic::DumpVector
, PLMD::gridtools::DumpGrid
- ONEOVERS2C2CUTOFF
: PLMD::membranefusion::fusionPoreNucleationP
, PLMD::membranefusion::memFusionP
- ones
: PLMD::contour::FindContourSurface
- Ones()
: PLMD::generic::Ones
- onStep()
: PLMD::ActionForInterface
, PLMD::ActionPilot
, PLMD::ActionToPutData
, PLMD::DomainDecomposition
- Op
: PLMD::isdb::CS2Backbone
- open()
: PLMD::FileBase
, PLMD::IFile
, PLMD::OFile
- open_file_read
: PLMD::molfile::molfile_plugin_t
- open_file_write
: PLMD::molfile::molfile_plugin_t
- OpenMPVars()
: PLMD::OpenMP::OpenMPVars
- operation
: PLMD::lepton::CompiledExpression
, PLMD::lepton::ExpressionTreeNode
- operations
: PLMD::lepton::ExpressionProgram
- Operator
: PLMD::lepton::ParseToken
- operator bool()
: PLMD::DomainDecomposition::DomainComms
, PLMD::FileBase
, PLMD::GridBase::AcceleratorHandler
, PLMD::Plumed
, PLMD::TypesafePtr
- operator const char *()
: PLMD::Plumed::CString
- operator plumed()
: PLMD::Plumed
- operator!=
: PLMD::AtomNumber
, PLMD::lepton::ExpressionTreeNode
, PLMD::lepton::Operation
, PLMD::Plumed
- operator()()
: PLMD::colvar::PathMSDBase::imgOrderByDist
, PLMD::colvar::PathMSDBase::imgOrderBySimilarity
, PLMD::function::FuncPathGeneral::pairordering
, PLMD::function::FuncPathMSD::ordering
, PLMD::function::FuncPathMSD::pairordering
, PLMD::Matrix< T >
, PLMD::maze::tls::delete_ptr
, PLMD::Plumed::rethrow_nested
, PLMD::Plumed::rethrow_not_nested
, PLMD::switchContainers::leptonSwitch::funcAndDeriv
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator*()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::Matrix< T >
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator*=()
: PLMD::Matrix< T >
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator+()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator++()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
- operator+=()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::Matrix< T >
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator-()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator--()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
- operator-=()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::Matrix< T >
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
- operator->()
: PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::GridBase::AcceleratorHandler
- operator/
: PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
- operator/=()
: PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
- operator<
: PLMD::AtomNumber
, PLMD::Plumed
- operator<<
: PLMD::Citations
, PLMD::Exception
, PLMD::ExceptionDebug
, PLMD::ExceptionError
, PLMD::ExceptionRegisterError
, PLMD::ExceptionTypeError
, PLMD::Matrix< T >
, PLMD::OFile
, PLMD::PDB
, PLMD::Random
, PLMD::Register
, PLMD::Stopwatch
, PLMD::Subprocess
, PLMD::TensorGeneric< n, m >
, PLMD::VectorGeneric< n >
- operator<<=()
: PLMD::Exception::Throw
- operator<=
: PLMD::AtomNumber
, PLMD::Plumed
- operator=()
: PLMD::Action
, PLMD::Communicator
, PLMD::DLLoader
, PLMD::Exception
, PLMD::FileBase
, PLMD::gch::detail::allocator_inliner< Allocator, false >
, PLMD::gch::detail::allocator_inliner< Allocator, true >
, PLMD::gch::detail::allocator_interface< Allocator >
, PLMD::gch::detail::inline_storage< T, InlineCapacity >
, PLMD::gch::detail::inline_storage< T, 0 >
, PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >
, PLMD::gch::detail::small_vector_base< Allocator, InlineCapacity >::stack_temporary
, PLMD::gch::detail::small_vector_data< Pointer, SizeT, T, InlineCapacity >
, PLMD::gch::detail::small_vector_data< Pointer, SizeT, T, 0 >
, PLMD::gch::detail::small_vector_data_base< Pointer, SizeT >
, PLMD::gch::small_vector< T, InlineCapacity, Allocator >
, PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::GridBase::AcceleratorHandler
, PLMD::lepton::AsmJitRuntimePtr
, PLMD::lepton::CompiledExpression
, PLMD::lepton::ExpressionProgram
, PLMD::lepton::ExpressionTreeNode
, PLMD::Matrix< T >
, PLMD::OpenMP::OpenMPVars
, PLMD::Plumed::add_buffer_to< T >
, PLMD::Plumed::CString
, PLMD::Plumed
, PLMD::Plumed::SafePtr
, PLMD::PlumedHandle
, PLMD::Stopwatch::Handler
, PLMD::Stopwatch
, PLMD::Subprocess::Handler
, PLMD::switchContainers::leptonSwitch::funcAndDeriv
, PLMD::Tools::CriticalSectionWithKey< Key >::Handler
, PLMD::TypesafePtr
, PLMD::ves::CoeffsMatrix
, PLMD::ves::CoeffsVector
, PLMD::ves::FermiSwitchingFunction
, PLMD::ves::LinearBasisSetExpansion
- operator==
: PLMD::AtomNumber
, PLMD::lepton::ExpressionTreeNode
, PLMD::lepton::Operation
, PLMD::Plumed
- operator>
: PLMD::AtomNumber
, PLMD::Plumed
- operator>=
: PLMD::AtomNumber
, PLMD::Plumed
- operator>>
: PLMD::Random
- operator[]()
: PLMD::gch::small_vector< T, InlineCapacity, Allocator >
, PLMD::gch::small_vector_iterator< Pointer, DifferenceType >
, PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_row
, PLMD::MatrixSquareBracketsAccess< T, C, I, J >
, PLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row
, PLMD::mdMemoryView< N, STRIDE >
, PLMD::MemoryView< N >
, PLMD::Tools::FastStringUnorderedMap< T >
, PLMD::VectorGeneric< n >
, PLMD::ves::CoeffsVector
- OPESexpanded()
: PLMD::opes::OPESexpanded
- OPESmetad()
: PLMD::opes::OPESmetad< mode >
- opt
: plumed_safeptr
, plumed_safeptr_x
- opt_
: PLMD::maze::Optimizer
- Opt_Adam()
: PLMD::ves::Opt_Adam
- Opt_BachAveragedSGD()
: PLMD::ves::Opt_BachAveragedSGD
- Opt_Dummy()
: PLMD::ves::Opt_Dummy
- opt_pntrs_
: PLMD::maze::OptimizerBias
- Opt_RobbinsMonroSGD()
: PLMD::ves::Opt_RobbinsMonroSGD
- opt_value_
: PLMD::maze::Optimizer
- OPTIMAL
: PLMD::RMSD
- OPTIMAL_FAST
: PLMD::RMSD
- optimalAlignment()
: PLMD::RMSD
- optimalAlignment_DDistDRef()
: PLMD::RMSD
- optimalAlignment_DDistDRef_Rot_DRotDPos()
: PLMD::RMSD
- optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef()
: PLMD::RMSD
- optimalAlignment_Fit()
: PLMD::RMSD
- optimalAlignment_PCA()
: PLMD::RMSD
- optimalAlignment_Rot()
: PLMD::RMSD
- optimalAlignment_Rot_DRotDRr01()
: PLMD::RMSD
- optimalAlignment_SOMA()
: PLMD::RMSD
- optimalAlignmentWithCloseStructure()
: PLMD::RMSD
- optimization_threshold_
: PLMD::ves::VesBias
- optimize()
: PLMD::dimred::ArrangePoints
, PLMD::dimred::SMACOF
, PLMD::lepton::ParsedExpression
, PLMD::maze::Memetic
, PLMD::maze::Optimizer
, PLMD::maze::Random_Acceleration_MD
, PLMD::maze::Random_Walk
, PLMD::maze::Simulated_Annealing
, PLMD::maze::Steered_MD
- optimize_coeffs_
: PLMD::ves::VesBias
- optimizeCoeffs()
: PLMD::ves::VesBias
- optimized_step_
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- Optimizer()
: PLMD::maze::Optimizer
, PLMD::ves::Optimizer
- optimizer_
: PLMD::maze::OptimizerBias
- optimizer_pntr_
: PLMD::ves::VesBias
- optimizer_stride_
: PLMD::maze::Optimizer
- OptimizerBias()
: PLMD::maze::OptimizerBias
- optional
: PLMD::Keywords::KeyType
- options
: PLMD::Action
, PLMD::metatensor::vesin::cpu::GrowableNeighborList
- optsigmamean_stride_
: PLMD::isdb::Caliber
, PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- orbital_energies
: PLMD::molfile::molfile_qm_wavefunction_t
- orbital_ids
: PLMD::molfile::molfile_qm_wavefunction_t
- order
: PLMD::function::Bessel
- origin
: PLMD::molfile::molfile_volumetric_t
, PLMD::volumes::VolumeAround
, PLMD::volumes::VolumeCavity
, PLMD::volumes::VolumeInCylinder
, PLMD::volumes::VolumeInSphere
, PLMD::volumes::VolumeTetrapore
- orthorombic
: PLMD::Pbc
- oss
: PLMD::OFile
- out
: PLMD::CLToolMain
- out_
: PLMD::sizeshape::position_linear_proj
- out_coupling_
: PLMD::eds::EDS
- out_observable_
: PLMD::fisst::FISST
- out_observable_name_
: PLMD::fisst::FISST
- out_of_bounds()
: PLMD::maze::Memetic
- out_restart_
: PLMD::eds::EDS
, PLMD::fisst::FISST
- out_restart_name_
: PLMD::eds::EDS
, PLMD::fisst::FISST
- OuterProduct()
: PLMD::matrixtools::OuterProduct
- outhills
: PLMD::function::FuncSumHills
- outhisto
: PLMD::function::FuncSumHills
- OUTLIERS
: PLMD::isdb::Metainference
, PLMD::isdb::MetainferenceBase
- output
: PLMD::generic::EffectiveEnergyDrift
- output_filename
: PLMD::drr::UIestimator::UIestimator
- output_fmt_
: PLMD::ves::CoeffsBase
- output_freq
: PLMD::drr::UIestimator::UIestimator
- output_grid
: PLMD::gridtools::InterpolateGrid
- output_of_each_layer
: PLMD::function::annfunc::ANN
- output_type
: PLMD::fourier::FourierTransform
- OutputBasisFunctions()
: PLMD::ves::OutputBasisFunctions
- OutputCluster()
: PLMD::clusters::OutputCluster
- outputComponentExists()
: PLMD::Keywords
- OutputFesBias()
: PLMD::ves::OutputFesBias
- outputForces
: PLMD::bias::Bias
- OutputTargetDistribution()
: PLMD::ves::OutputTargetDistribution
- ovdd_
: PLMD::isdb::EMMI
- ovfilename_
: PLMD::isdb::EMMI
- ovmd_
: PLMD::isdb::EMMI
- ovmd_ave_
: PLMD::isdb::EMMI
- ovmd_der_
: PLMD::isdb::EMMI
- ovstride_
: PLMD::isdb::EMMI
1.8.17