NAMD: Class Members

_ | a | b | c | d | e | f | g | h | i | j | k | l | m | n | o | p | q | r | s | t | u | v | w | x | y | z | ~

Here is a list of all class members with links to the classes they belong to:

- _ -

_get_keyval_scalar_proto_() : colvarparse
_get_keyval_vector_proto_() : colvarparse
_hasNewAtoms : Patch
_iter : OptPmePencil< T >

- a -

a : Lattice, sortop_base, NL_Msm_t, ComputeMsmMgr
A : indexed_vdw_pair, vdw_pair_params, go_pair, LJTable::TableEntry
A14 : indexed_vdw_pair, vdw_pair_params
a_cut : GBISParamStruct
a_f : NL_Msm_t
a_p() : Lattice
a_r() : Lattice
a_total : nodesort
aa : thole
aaAngleExp : SimParameters
abuffer : msm::Array< T >
acc_force() : colvar_grid_gradient
acc_grad() : colvar_grid_gradient
acc_value() : colvar_grid_scalar
accelMDalpha : SimParameters
accelMDDebugOn : SimParameters
accelMDdihe : SimParameters
accelMDdoDihe : ComputeHomeTuples< T, S, P >
accelMDdual : SimParameters
accelMDdVAverage : Controller
accelMDE : SimParameters
accelMDFirstStep : SimParameters
accelMDLastStep : SimParameters
accelMDOn : SimParameters, ComputeNonbondedUtil
accelMDOutFreq : SimParameters
accelMDRescaleFactor : ControllerBroadcasts
accelMDTalpha : SimParameters
accelMDTE : SimParameters
acceptor : colvar::h_bond
Accumulate() : ALambdaManager, ALambdaControl
acf : colvar
acf_colvar_name : colvar
acf_coor : colvar
acf_length : colvar
acf_nframes : colvar
acf_normalize : colvar
acf_notset : colvar
acf_offset : colvar
acf_outfile : colvar
acf_p2coor : colvar
acf_stride : colvar
acf_type : colvar
acf_type_e : colvar
acf_v_history : colvar
acf_v_history_p : colvar
acf_vel : colvar
acf_x_history : colvar
acf_x_history_p : colvar
ackAtomsToHomePatchProcs() : ParallelIOMgr
activate_pencils() : OptPmeMgr, ComputePmeMgr
active : msm::FoldFactor
activePatches : ComputeNonbondedCUDA
actual_value : colvar, colvar_grid< T >
adaptTempAutoDt : SimParameters, Controller
adaptTempBetaMax : Controller
adaptTempBetaMin : Controller
adaptTempBetaN : Controller
adaptTempBin : Controller
adaptTempBins : SimParameters, Controller
adaptTempCg : Controller
adaptTempCgamma : SimParameters
adaptTempDBeta : Controller
adaptTempDebug : SimParameters
adaptTempDt : SimParameters, Controller
adaptTempDTave : Controller
adaptTempDTavenum : Controller
adaptTempDtMax : Controller
adaptTempDtMin : Controller
adaptTemperature : ControllerBroadcasts
adaptTempFirstStep : SimParameters
adaptTempFreq : SimParameters
adaptTempInFile : SimParameters
adaptTempInit() : Controller
adaptTempLangevin : SimParameters
adaptTempLastStep : SimParameters
adaptTempOn : SimParameters
adaptTempOutFreq : SimParameters
adaptTempPotEnergyAve : Controller
adaptTempPotEnergyAveDen : Controller
adaptTempPotEnergyAveNum : Controller
adaptTempPotEnergySamples : Controller
adaptTempPotEnergyVar : Controller
adaptTempPotEnergyVarNum : Controller
adaptTempRandom : SimParameters
adaptTempRescale : SimParameters
adaptTempRestartFile : SimParameters, Controller
adaptTempRestartFreq : SimParameters
adaptTempT : Sequencer, Controller
adaptTempTmax : SimParameters
adaptTempTmin : SimParameters
adaptTempUpdate() : Sequencer, Controller
adaptTempWriteRestart() : Controller
Add() : ARestraintManager, ALambdaManager, AGroup
add() : UniqueSortedArray< Elem >, UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ResizeArray< Elem >, SubmitReduction, MigrateAtomsCombinedMsg, MGridforceParamsList
add14Type() : VDWTable
add_atom() : colvarmodule::atom_group
add_bias_force() : colvar
add_colvar() : colvarbias
add_constant() : colvar_grid< T >
add_element() : ConfigList
add_energy() : colvarproxy_namd, colvarproxy
add_grid() : colvar_grid< T >
add_keyword() : colvarparse
addAngle() : GenericMol
addAtom() : GenericMol
addBond() : GenericMol
addCharge() : MsmC1HermiteBlock, MsmBlock
addClient() : GlobalMasterServer
addDihedral() : GenericMol
addEnergy() : GlobalMasterEasy
addForce() : GlobalMasterFreeEnergy, GlobalMasterEasy
AddForces() : ARestraintManager
addForceToMomentum() : Sequencer, HomePatch
addIndex() : Pairlists
addMovDragToPosition() : Sequencer
addPairGaussType2() : PairTable
addPairLJType2() : PairTable
addPotential() : MsmC1HermiteBlock, MsmBlock, msm::PatchData, ComputeMsmMgr
addPotentialC1Hermite() : msm::PatchData
address() : colvar_grid< T >
addRotDragToPosition() : Sequencer
addToRemoteSequenceNumber : ReductionSet
addToSubgridsFlat() : GridforceFullSubGrid
addType() : VDWTable, DihedralTable, AngleTable, BondTable, AtomTable
addVelocityToPosition() : Sequencer, HomePatch
addVirialContrib() : ComputeMsmMgr
ADiheRestraint() : ADiheRestraint
ADistRestraint() : ADistRestraint
adjustBackgroundLoadAndComputeAverage() : Rebalancer
af : TuplePatchElem
AGroup() : AGroup
aid : ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeConsForceMsg, CollectionMgr::CollectVectorInstance, CollectVectorVarMsg, CollectVectorMsg
aid_size : CollectVectorMsg
ALambdaControl() : ALambdaControl
ALambdaManager() : ALambdaManager
alchDecouple : SimParameters, ComputeNonbondedUtil
alchDispLambda : SimParameters, ComputeNonbondedUtil
alchDroppedAngles : Molecule
alchDroppedDihedrals : Molecule
alchDroppedImpropers : Molecule
alchElecLambda : SimParameters, ComputeNonbondedUtil
alchElecLambdaStart : SimParameters, ComputeNonbondedUtil
alchEnsembleAvg : SimParameters
alchEquilSteps : SimParameters
alchFepElecOn : SimParameters
alchFepOn : SimParameters, ComputeNonbondedUtil
alchFepWCADispOn : SimParameters
alchFepWCArcut1 : SimParameters
alchFepWCArcut2 : SimParameters
alchFepWCArcut3 : SimParameters
alchFepWCARepuOn : SimParameters
alchFepWhamOn : SimParameters
alchLambda : SimParameters, ComputeNonbondedUtil
alchLambda2 : SimParameters, ComputeNonbondedUtil
alchMethod : SimParameters
alchOn : SimParameters
alchOutFile : SimParameters
alchOutFreq : SimParameters
alchRepLambda : SimParameters, ComputeNonbondedUtil
alchTemp : SimParameters
alchThermIntOn : SimParameters, ComputeNonbondedUtil
alchVdwLambdaEnd : SimParameters, ComputeNonbondedUtil
alchVdwShiftCoeff : SimParameters, ComputeNonbondedUtil
alen : msm::Array< T >
Alg7() : Alg7
AlgNbor() : AlgNbor
algorithm() : Sequencer, Controller
AlgRecBisection() : AlgRecBisection
AlignVector() : AlignVector
allAtoms : MovePatchAtomsMsg
allExclCnt : ExclusionSignature
alloc() : colvarmodule::matrix2d< T, outer_length, inner_length >
allocateCids() : ComputeMap
allocateMap() : AtomMap
allowed_keywords : colvarparse
allPes : ProxyNodeAwareSpanningTreeMsg
allTuples : ExclusionSignature
alpha : drude_constants
alpha_angles() : colvar::alpha_angles
alpha_cutoff : SimParameters
alpha_max : SimParameters, GBISParamStruct
alphai : nbthole_pair_value, indexed_nbthole_pair, nbthole_pair_params
alphaj : nbthole_pair_value, indexed_nbthole_pair, nbthole_pair_params
alternatelocation() : PDBAtom
amax : msm::Array< T >
amberOn : SimParameters
amd_reduction : OptPmeXPencil, Controller, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
amdf : Results
analyse() : colvarbias, colvar
analyze() : colvarmodule
AnAngleRestraint() : AnAngleRestraint
angle : colvar::angle, lphost, angle_params
angle_array : Parameters
angle_type : angle
AngleAt1 : parm
AngleAt2 : parm
AngleAt3 : parm
angleCnt : AtomSignature
AngleElem : AngleElem, Molecule
angleEnergyIndex : AngleElem
AngleHAt1 : parm
AngleHAt2 : parm
AngleHAt3 : parm
AngleHNum : parm
AngleNum : parm
angleSigIndices : AtomSigInfo
angleSigs : AtomSignature
AnisoElem : AnisoElem, Molecule
anisoEnergyIndex : AnisoElem
ANISOU : PDBData
ANTERP : MsmTimer
anterpolation() : msm::PatchData
anterpolationC1Hermite() : msm::PatchData
APosRestraint() : APosRestraint
append() : msm::Array< T >, ResidueLookupElem, CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
appForces : GlobalMaster
appForcesChanged : GlobalMaster
applied_forces : colvarproxy_namd
appliedForces() : GlobalMaster
apply_colvar_force() : colvarmodule::atom_group
apply_constraints() : colvarvalue
apply_force() : colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvarmodule::atom_group, colvarmodule::atom
apply_forces() : colvarmodule::atom_group
apply_rotation() : colvarmodule::atom_group
apply_transform() : Lattice
apply_translation() : colvarmodule::atom_group
Approx : ComputeMsmMgr
approx : NL_Msm_t, ComputeMsmMgr
ARestraint() : ARestraint
ARestraintManager() : ARestraintManager
array : CkCallbackWrapper, colvarmodule::matrix2d< T, outer_length, inner_length >, colvarmodule::vector1d< T, length >
Array() : msm::Array< T >, Array< Elem, Size >
assign() : Rebalancer
assign_angle_index() : Parameters
assign_bond_index() : Parameters
assign_crossterm_index() : Parameters
assign_dihedral_index() : Parameters
assign_improper_index() : Parameters
assign_vdw_index() : Parameters
assignBaseNode() : PatchMap
assignNode() : PatchMap
assignNodeToPatch() : WorkDistrib
assignPatches() : ComputeNonbondedCUDA
assignToPatch() : PatchMap
atoBool() : MGridforceParamsList
ATOM : PDBData
atom : PDB, colvarmodule::atom, MovePatchesMsg, NL_Msm_t, colvarmodule
atom1 : Exclusion, thole, aniso, lphost, crossterm, improper, dihedral, angle, bond
atom1name : nbthole_pair_params, table_pair_params, vdw_pair_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params
atom1wild : dihedral_params
atom2 : Exclusion, thole, aniso, lphost, crossterm, improper, dihedral, angle, bond
atom2name : nbthole_pair_params, table_pair_params, vdw_pair_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params
atom2wild : dihedral_params
atom3 : thole, aniso, lphost, crossterm, improper, dihedral, angle
atom3name : crossterm_params, improper_params, dihedral_params, angle_params
atom3wild : dihedral_params
atom4 : thole, aniso, lphost, crossterm, improper, dihedral
atom4name : crossterm_params, improper_params, dihedral_params
atom4wild : dihedral_params
atom5 : crossterm
atom5name : crossterm_params
atom6 : crossterm
atom6name : crossterm_params
atom7 : crossterm
atom7name : crossterm_params
atom8 : crossterm
atom8name : crossterm_params
atom_const_iter : colvarmodule
atom_f : NL_Msm_t
atom_group : colvarmodule::atom_group, colvarmodule
atom_groups : colvar::cvc
atom_ids : colvar
atom_iter : colvarmodule
atom_pos : colvarmodule
atom_type_name() : Parameters
atomChainTypes : Molecule
atomcharge() : Molecule
atomFixed : CompAtomExt
atomic_gradients : colvar
atomid : MoveAtomMsg
atomID : HydrogenGroupID, position_index, TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
atomIdBegin : GlobalMaster
atomIdEnd : GlobalMaster
atomIndex : ResidueLookupElem
atomList : MoveInputAtomsMsg
atomMap : Node, ComputeNonbondedCUDA, ComputeHomeTuples< T, S, P >
AtomMap() : AtomMap
atomMapper : Patch
AtomMapper : AtomMapper, AtomMap
atommass() : Molecule
atomname : atom_name_info, vdw_params
atomnameIdx : AtomNameIdx
atomNameIdx : OutputAtomRecord::shortVals, BasicAtomInfo
AtomNames : parm
atomPositionBegin : GlobalMaster
AtomRes : parm
atoms : PDB, colvar::rmsd, colvar::orientation, colvar::eigenvector, colvar::gyration
atoms_1to4() : Molecule
atoms_cog : colvar::orientation
atomsCnt : ClusterSizeMsg, ClusterElem
atomsCntList : AtomsCntPerPatchMsg
atomSigIdx : OutputAtomRecord::integerVals, BasicAtomInfo
AtomSigInfo() : AtomSigInfo
AtomSignature() : AtomSignature
atomsInGroup : HydrogenGroupID, OutputAtomRecord::integerVals
atomsInMigrationGroup : HydrogenGroupID, OutputAtomRecord::integerVals
atomSort_0_sortValues__ : ComputeNonbondedWorkArrays
atomSort_1_sortValues__ : ComputeNonbondedWorkArrays
AtomSym : parm
AtomTree : parm
atomtype : atom_name_info
atomtypeIdx : AtomNameIdx
atomTypeIdx : OutputAtomRecord::shortVals, BasicAtomInfo
atomUpdate() : ComputePatchPair, ComputePatch, ComputeNonbondedCUDA, ComputeLCPO, ComputeHomeTuples< T, S, P >, ComputeHomePatches, ComputeHomePatch, Compute
atomvdwtype() : Molecule
AUTHOR : PDBData
auxFilename : SimParameters
available : processorInfo
AVector() : AVector
average() : colvar_grid_gradient
averageLoad : Rebalancer
avg_count : Controller
avgPlLen : ProxyDataMsg
avgPositionBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, TuplePatchElem, PatchElem
avgPositionBoxClosed() : Patch
avgPositionComputeList : Patch
avgPositionList : ProxyDataMsg
avgPositionPtrBegin : Patch
avgPositionPtrEnd : Patch
awaitBOCCheckIn() : Node
awaken() : Sequencer, Controller, BroadcastClient, BackEnd
awakenSequencers() : LdbCoordinator
axis : colvar::spin_angle, colvar::tilt, colvar::inertia_z, colvar::distance_z
axis_norm : colvar::distance_z

- b -

b : Lattice, netint
B : indexed_vdw_pair, vdw_pair_params, go_pair, LJTable::TableEntry
B14 : indexed_vdw_pair, vdw_pair_params
b_1site_force : colvar::dihedral, colvar::angle, colvar::distance_z, colvar::distance
b_analysis : colvarmodule
b_anisotropic : colvar::coordnum
b_center : colvarmodule::atom_group
b_chg_centers : colvarbias_harmonic
b_chg_force_k : colvarbias_harmonic
b_debug_gradients : colvarmodule::rotation, colvar::cvc
b_dummy : colvarmodule::atom_group
b_fit_gradients : colvarmodule::atom_group
b_group2_center_only : colvar::coordnum
b_hills_traj : colvarbias_meta
b_inverse_gradients : colvar::cvc, colvar
b_Jacobian_derivative : colvar::cvc
b_Jacobian_force : colvar
b_linear : colvar
b_no_PBC : colvar::distance_z, colvar::distance
b_p() : Lattice
b_periodic : colvar::cvc, colvar
b_r() : Lattice
b_rotate : colvarmodule::atom_group
b_total : nodesort
b_user_defined_fit : colvarmodule::atom_group
backgroundLoad : processorInfo
backup_file() : colvarproxy_namd, colvarproxy, colvarmodule
backward_fft() : OptPmeXPencil, OptPmeYPencil, OptPmeZPencil, PmeXPencil, PmeYPencil, PmeZPencil
backward_plan : OptPmeXPencil, PmeXPencil
backward_subset_fft() : PmeYPencil
barrier() : LdbCoordinator, BackEnd
base_init() : OptPmePencil< T >, PmePencil< T >
basenode() : PatchMap
basePatchIDList() : PatchMap
basePriority : Compute
bcastHydroBasedCounter() : ParallelIOMgr
bcastMolInfo() : ParallelIOMgr
bd : MsmBlockKernel< Vtype, Mtype >
begin() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, Array< Elem, Size >
benchTimestep : SimParameters
berendsenPressure() : Sequencer, Controller
berendsenPressure_avg : Controller
berendsenPressure_count : Sequencer, Controller
berendsenPressureCompressibility : SimParameters
berendsenPressureFreq : SimParameters
berendsenPressureOn : SimParameters
berendsenPressureRelaxationTime : SimParameters
berendsenPressureTarget : SimParameters
beta : GBISParamStruct
bh : MoaData
bias_energy : colvarbias
bias_temperature : colvarbias_meta
biases : colvarmodule
bin : NL_Msm_t
bin_distance_from_boundaries() : colvar_grid< T >
bin_to_value_scalar() : colvar_grid< T >
binaryOutput : SimParameters
binaryRefine() : RefineTorusLB
binaryRestart : SimParameters
binAtomFile : SimParameters
binCoorFile : SimParameters
binfill : NL_Msm_t
binRefFile : SimParameters
binVelFile : SimParameters
block1 : PmeGrid
block2 : PmeGrid
block3 : PmeGrid
block_total : NL_Msm_t
blockAssign : ComputeMsmMgr
blockFlatIndex() : ComputeMsmMgr
BlockIndex() : msm::BlockIndex
blockIndex : MsmBlockKernel< Vtype, Mtype >
blockLevel : msm::Map
blockOfGridIndex() : msm::Map
blockOfGridIndexFold() : msm::Map
BOCCheckIn() : Node
BOID() : BOID
boltzmann() : colvarproxy_namd, colvarproxy, colvarmodule
bond_array : Parameters
bond_type : bond
BondAt1 : parm
BondAt2 : parm
bondCnt : AtomSignature
BondElem : BondElem, Molecule
bondEnergyIndex : BondElem
BondHAt1 : parm
BondHAt2 : parm
BondHNum : parm
BondNum : parm
bondSigIndices : AtomSigInfo
bondSigs : AtomSignature
BOOL : ParseOptions::DataElement
border : GridforceFullMainGrid
bornRad : ProxyGBISP2DataMsg, Patch, GBISParamStruct, ComputeNonbondedCUDA::patch_record
bornRadBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA::patch_record
bornRadBoxClosed() : Patch
bornRadComputeList : Patch
bornRadLen : ProxyGBISP2DataMsg
BothValid : CollectVectorVarMsg
Boundary : parm
Box : parm
Box<Owner,Data> : OwnerBox< Owner, Data >
boxClosed() : ProxyPatch, Patch, HomePatch
boxesOpen : Patch
brace_check() : colvarparse
brickDim() : Rebalancer
broadcast : Sequencer, Controller
broadcastClient : BroadcastClientElem
BroadcastClient() : BroadcastClient
BroadcastClientElem() : BroadcastClientElem
broadcastMgr : BOCgroup
BroadcastMgr : BroadcastMgr, BroadcastMsg
BroadcastMsg() : BroadcastMsg
broadcastSet : BOID
bsearch() : SortedArray< Elem >, SortableResizeArray< Elem >
bsx : msm::Map
bsy : msm::Map
bsz : msm::Map
bu : NL_Msm_t
buffer() : msm::GridFixed< T, N >, msm::Array< T >
build_atom_list() : colvar
build_constant_forces() : Molecule
build_constorque_params() : Molecule
build_constraint_params() : Molecule
build_exclusions() : ComputeNonbondedCUDA
build_exPressure_atoms() : Molecule
build_extra_bonds() : Molecule
build_fep_flags() : Molecule
build_fixed_atoms() : Molecule
build_force_table() : ComputeNonbondedCUDA
build_go_arrays() : Molecule
build_go_params() : Molecule
build_go_sigmas() : Molecule
build_go_sigmas2() : Molecule
build_gridforce_params() : Molecule
build_gro_pair() : Molecule
build_langevin_params() : Molecule
build_lj_table() : ComputeNonbondedCUDA
build_matrix() : colvarmodule::rotation
build_movdrag_params() : Molecule
build_rotdrag_params() : Molecule
build_stirred_atoms() : Molecule
buildProxySpanningTree() : ProxyMgr
buildProxySpanningTree2() : ProxyMgr
buildSpanningTree() : HomePatch
buildSpanningTree0() : ProxyMgr
buildSpanTree() : ReductionMgr
buildSubgridsFlat() : GridforceFullMainGrid
buildTuples() : ExclusionSignature
bv : NL_Msm_t
bw : NL_Msm_t
bytesPerAtom : Rebalancer

- c -

c : Lattice, Rebalancer::pcpair, CrosstermValue, ComputeNonbondedCUDA::compute_record, ComputeMsmMgr
c0 : ComputeNonbondedUtil
c1 : ComputeNonbondedUtil
c12pair : GroLJPair
C1HERMITE : ComputeMsmMgr
C1Matrix() : C1Matrix
C1Vector() : C1Vector
c3 : ComputeNonbondedUtil
c5 : ComputeNonbondedUtil
c6 : ComputeNonbondedUtil
c6pair : GroLJPair
c7 : ComputeNonbondedUtil
c8 : ComputeNonbondedUtil
c_array() : colvarmodule::matrix2d< T, outer_length, inner_length >, colvarmodule::vector1d< T, length >
c_p() : Lattice
c_r() : Lattice
c_total : nodesort
calc() : colvarmodule, colvar
calc_acf() : colvar
calc_apply_roto_translation() : colvarmodule::atom_group
calc_coor_acf() : colvar
calc_error() : ComputeNonbondedUtil
calc_fit_gradients() : colvarmodule::atom_group
calc_force_invgrads() : colvar::rmsd, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::gyration, colvar::distance_xy, colvar::distance_z, colvar::distance, colvar::cvc
calc_gradients() : colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc
calc_hills() : colvarbias_meta
calc_hills_force() : colvarbias_meta
calc_Jacobian_derivative() : colvar::rmsd, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::gyration, colvar::distance_xy, colvar::distance_z, colvar::distance, colvar::cvc
calc_optimal_rotation() : colvarmodule::rotation
calc_p2coor_acf() : colvar
calc_pair() : ComputeNonbondedUtil
calc_pair_energy() : ComputeNonbondedUtil
calc_pair_energy_fep() : ComputeNonbondedUtil
calc_pair_energy_fullelect() : ComputeNonbondedUtil
calc_pair_energy_fullelect_fep() : ComputeNonbondedUtil
calc_pair_energy_fullelect_go() : ComputeNonbondedUtil
calc_pair_energy_fullelect_int() : ComputeNonbondedUtil
calc_pair_energy_fullelect_les() : ComputeNonbondedUtil
calc_pair_energy_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_energy_fullelect_tabener() : ComputeNonbondedUtil
calc_pair_energy_fullelect_ti() : ComputeNonbondedUtil
calc_pair_energy_go() : ComputeNonbondedUtil
calc_pair_energy_int() : ComputeNonbondedUtil
calc_pair_energy_les() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_fep() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_go() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_int() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_les() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_tabener() : ComputeNonbondedUtil
calc_pair_energy_merge_fullelect_ti() : ComputeNonbondedUtil
calc_pair_energy_pprof() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_fep() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_go() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_les() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_tabener() : ComputeNonbondedUtil
calc_pair_energy_slow_fullelect_ti() : ComputeNonbondedUtil
calc_pair_energy_tabener() : ComputeNonbondedUtil
calc_pair_energy_ti() : ComputeNonbondedUtil
calc_pair_fullelect() : ComputeNonbondedUtil
calc_pair_fullelect_go() : ComputeNonbondedUtil
calc_pair_fullelect_les() : ComputeNonbondedUtil
calc_pair_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_fullelect_tabener() : ComputeNonbondedUtil
calc_pair_fullelect_ti() : ComputeNonbondedUtil
calc_pair_go() : ComputeNonbondedUtil
calc_pair_les() : ComputeNonbondedUtil
calc_pair_merge_fullelect() : ComputeNonbondedUtil
calc_pair_merge_fullelect_go() : ComputeNonbondedUtil
calc_pair_merge_fullelect_les() : ComputeNonbondedUtil
calc_pair_merge_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_merge_fullelect_tabener() : ComputeNonbondedUtil
calc_pair_merge_fullelect_ti() : ComputeNonbondedUtil
calc_pair_pprof() : ComputeNonbondedUtil
calc_pair_slow_fullelect() : ComputeNonbondedUtil
calc_pair_slow_fullelect_go() : ComputeNonbondedUtil
calc_pair_slow_fullelect_les() : ComputeNonbondedUtil
calc_pair_slow_fullelect_pprof() : ComputeNonbondedUtil
calc_pair_slow_fullelect_tabener() : ComputeNonbondedUtil
calc_pair_slow_fullelect_ti() : ComputeNonbondedUtil
calc_pair_tabener() : ComputeNonbondedUtil
calc_pair_ti() : ComputeNonbondedUtil
calc_runave() : colvar
calc_self() : ComputeNonbondedUtil
calc_self_energy() : ComputeNonbondedUtil
calc_self_energy_fep() : ComputeNonbondedUtil
calc_self_energy_fullelect() : ComputeNonbondedUtil
calc_self_energy_fullelect_fep() : ComputeNonbondedUtil
calc_self_energy_fullelect_go() : ComputeNonbondedUtil
calc_self_energy_fullelect_int() : ComputeNonbondedUtil
calc_self_energy_fullelect_les() : ComputeNonbondedUtil
calc_self_energy_fullelect_pprof() : ComputeNonbondedUtil
calc_self_energy_fullelect_tabener() : ComputeNonbondedUtil
calc_self_energy_fullelect_ti() : ComputeNonbondedUtil
calc_self_energy_go() : ComputeNonbondedUtil
calc_self_energy_int() : ComputeNonbondedUtil
calc_self_energy_les() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_fep() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_go() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_int() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_les() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_pprof() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_tabener() : ComputeNonbondedUtil
calc_self_energy_merge_fullelect_ti() : ComputeNonbondedUtil
calc_self_energy_pprof() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_fep() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_go() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_les() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_pprof() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_tabener() : ComputeNonbondedUtil
calc_self_energy_slow_fullelect_ti() : ComputeNonbondedUtil
calc_self_energy_tabener() : ComputeNonbondedUtil
calc_self_energy_ti() : ComputeNonbondedUtil
calc_self_fullelect() : ComputeNonbondedUtil
calc_self_fullelect_go() : ComputeNonbondedUtil
calc_self_fullelect_les() : ComputeNonbondedUtil
calc_self_fullelect_pprof() : ComputeNonbondedUtil
calc_self_fullelect_tabener() : ComputeNonbondedUtil
calc_self_fullelect_ti() : ComputeNonbondedUtil
calc_self_go() : ComputeNonbondedUtil
calc_self_les() : ComputeNonbondedUtil
calc_self_merge_fullelect() : ComputeNonbondedUtil
calc_self_merge_fullelect_go() : ComputeNonbondedUtil
calc_self_merge_fullelect_les() : ComputeNonbondedUtil
calc_self_merge_fullelect_pprof() : ComputeNonbondedUtil
calc_self_merge_fullelect_tabener() : ComputeNonbondedUtil
calc_self_merge_fullelect_ti() : ComputeNonbondedUtil
calc_self_pprof() : ComputeNonbondedUtil
calc_self_slow_fullelect() : ComputeNonbondedUtil
calc_self_slow_fullelect_go() : ComputeNonbondedUtil
calc_self_slow_fullelect_les() : ComputeNonbondedUtil
calc_self_slow_fullelect_pprof() : ComputeNonbondedUtil
calc_self_slow_fullelect_tabener() : ComputeNonbondedUtil
calc_self_slow_fullelect_ti() : ComputeNonbondedUtil
calc_self_tabener() : ComputeNonbondedUtil
calc_self_ti() : ComputeNonbondedUtil
calc_value() : colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
calc_vel_acf() : colvar
calcAtomsInEachPatch() : ParallelIOMgr
calcBlockWork() : ComputeMsmMgr
calcFullPair : ComputeNonbondedUtil
calcFullPairEnergy : ComputeNonbondedUtil
calcFullSelf : ComputeNonbondedUtil
calcFullSelfEnergy : ComputeNonbondedUtil
calcGBIS() : ComputeNonbondedUtil
calcGcutWork() : ComputeMsmMgr
calcMergePair : ComputeNonbondedUtil
calcMergePairEnergy : ComputeNonbondedUtil
calcMergeSelf : ComputeNonbondedUtil
calcMergeSelfEnergy : ComputeNonbondedUtil
calcPair : ComputeNonbondedUtil
calcPairEnergy : ComputeNonbondedUtil
calcSelf : ComputeNonbondedUtil
calcSelfEnergy : ComputeNonbondedUtil
calcSlowPair : ComputeNonbondedUtil
calcSlowPairEnergy : ComputeNonbondedUtil
calcSlowSelf : ComputeNonbondedUtil
calcSlowSelfEnergy : ComputeNonbondedUtil
calculate() : GlobalMasterTest, GlobalMasterTcl, GlobalMasterIMD, GlobalMaster, colvarproxy_namd
cb : CkCallbackWrapper
cb_energy : OptPmePencilInitMsgData
cbw_recvtrans : OptPmeXPencil
cellBasisVector1 : SimParameters
cellBasisVector2 : SimParameters
cellBasisVector3 : SimParameters
cellcenter : NL_Msm_t
cellcenter_f : NL_Msm_t
cellOrigin : SimParameters
cellvec1 : NL_Msm_t
cellvec1_f : NL_Msm_t
cellvec2 : NL_Msm_t
cellvec2_f : NL_Msm_t
cellvec3 : NL_Msm_t
cellvec3_f : NL_Msm_t
center : PatchMap, colvarbias_meta::hill, GridforceLiteGrid, GridforceFullBaseGrid
center_of_geometry() : colvarmodule::atom_group
center_of_mass() : colvarmodule::atom_group
center_ref_pos() : colvarmodule::atom_group
centers : colvarbias_meta::hill
centers_incr : colvarbias_harmonic
cg : PmeParticle, EwaldParticle
chain() : PDBAtom
change_configuration() : colvarmodule, colvarbias_harmonic, colvarbias
changedAtoms() : GlobalMaster
changedForces() : GlobalMaster
changedGroups() : GlobalMaster
charge : atom_constants, CompAtom, msm::AtomCoord, ComputeMsmSerialAtom, ComputeGBISAtom, ComputeFmmSerialAtom, ComputeExtAtom
chargeIdx : OutputAtomRecord::shortVals, BasicAtomInfo
Charges : parm
check() : GlobalMaster
check_consistency() : ParseOptions, colvar_grid< T >
check_keywords() : colvarparse
check_types() : colvarvalue
checkexcl() : Molecule
checkIn() : OwnerBox< Owner, Data >
checkMap() : PatchMap, ComputeMap, AtomMap
checkOut() : OwnerBox< Owner, Data >
checkpoint() : HomePatch
checkpoint_berendsenPressure_avg : Controller
checkpoint_berendsenPressure_count : Sequencer, Controller
checkpoint_langevinPiston_strainRate : Controller
checkpoint_lattice : Controller
checkpoint_smooth2_avg : Controller
checkpoint_stored : Controller
checksum : StreamMessage
child : Patch
cid : PatchMap, GBISParamStruct, Compute
Clear() : ALambdaManager, AGroup
clear() : UniqueSetRaw< Elem >, EntryGlob< Elem >, Entry< Elem >, UniqueSet< Elem >, ResizeArray< Elem >, msm::PriorityQueue< T >, MGridforceParamsList, HashPool< T >
clearChain() : EntryGlob< Elem >, Entry< Elem >
clearChanged() : GlobalMaster
clientAdd() : OwnerBox< Owner, Data >
clientClose() : OwnerBox< Owner, Data >
clientOpen() : OwnerBox< Owner, Data >
clientRemove() : OwnerBox< Owner, Data >
clients : GlobalMasterIMD
clipBlockToIndexRange() : msm::Map
clipBlockToIndexRangeFold() : msm::Map
clipIndexToLevel() : msm::Map
cloneCompute() : ComputeMap
close() : OwnerBox< Owner, Data >, Box< Owner, Data >
ClusterCoorElem() : ClusterCoorElem
ClusterElem() : ClusterElem
clusterId : ClusterCoorMsg, ClusterCoorElem, ClusterSizeMsg, ClusterElem
Cn1 : parm
Cn2 : parm
Cno : parm
cntRecvs : msm::PatchData
cntRecvsCharge : MsmBlockKernel< Vtype, Mtype >
cntRecvsPotential : MsmBlockKernel< Vtype, Mtype >
cntVirialContrib : ComputeMsmMgr
coeffs : colvar::dihedPC
COLDOn : SimParameters
COLDRate : SimParameters
COLDTemp : SimParameters
collection : Sequencer, Controller
CollectionMaster() : CollectionMaster
collectionMgr : BOCgroup
CollectionMgr() : CollectionMgr
CollectVectorInstance() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
COLUMNS : PDBData
columnsize : Parameters, ComputeNonbondedUtil
colvar() : colvar
colvar_centers : colvarbias_harmonic
colvar_centers_raw : colvarbias_harmonic
colvar_forces : colvarbias
colvar_grid() : colvar_grid< T >
colvar_grid_count() : colvar_grid_count
colvar_grid_gradient() : colvar_grid_gradient
colvar_grid_scalar() : colvar_grid_scalar
colvar_p() : colvarmodule
colvarbias() : colvarbias
colvarbias_abf() : colvarbias_abf
colvarbias_harmonic() : colvarbias_harmonic
colvarbias_histogram() : colvarbias_histogram
colvarbias_meta : colvarbias_meta, colvarbias_meta::hill
colvarmodule() : colvarmodule
colvarparse() : colvarparse
colvarproxy : colvarmodule
colvarproxy_namd() : colvarproxy_namd
colvars : Node, colvarproxy, colvarmodule, colvarbias
colvars_atoms : colvarproxy_namd
colvars_atoms_ncopies : colvarproxy_namd
colvarsOn : SimParameters
colvarvalue() : colvarvalue
COMM : MsmTimer
comm : colvarbias_meta
commOnly : SimParameters, ComputeNonbondedUtil
comMove : SimParameters
Communicate() : Communicate
communicate_forces() : colvarbias, colvar
Communication : colvarbias_meta
compare() : ProxyUsageKey, HashPoolAdaptorT< T >, colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
compareChecksums() : Controller
COMPND : PDBData
compute : MsmC1HermiteGridCutoff, MsmGridCutoff, MsmGridCutoffKernel< Vtype, Mtype >, ComputeMsmMgr, ComputeMap, LocalWorkMsg, OptPmeSubComputeMsg
Compute() : Compute
compute_a() : GridforceFullBaseGrid
compute_b() : GridforceFullSubGrid, GridforceFullMainGrid, GridforceFullBaseGrid
compute_d2V() : GridforceFullBaseGrid
compute_d3V() : GridforceFullBaseGrid
compute_derivative_grids() : GridforceLiteGrid
compute_dV() : GridforceFullBaseGrid
compute_energy() : PmeKSpace
compute_energy_orthogonal_helper() : PmeKSpace
compute_energy_orthogonal_subset() : PmeKSpace
compute_forces() : PmeRealSpace, OptPmeRealSpace
compute_forces_order4_partial() : PmeRealSpace
compute_specialized() : MsmC1HermiteGridCutoff
compute_V() : GridforceFullBaseGrid
compute_VdV() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
compute_wts() : GridforceLiteGrid
ComputeAngles() : ComputeAngles
ComputeAniso() : ComputeAniso
computeArray : LdbCoordinator
computeAverage() : Rebalancer
computeBgPairHeap : Rebalancer
computeBgSelfHeap : Rebalancer
ComputeBonds() : ComputeBonds
computeChecksum : Controller
ComputeConsForce() : ComputeConsForce
ComputeConsForceMsg() : ComputeConsForceMsg
ComputeConsTorque() : ComputeConsTorque
ComputeCrossterms() : ComputeCrossterms
ComputeCylindricalBC() : ComputeCylindricalBC
ComputeData() : ComputeMap::ComputeData
ComputeDihedrals() : ComputeDihedrals
ComputeDPMEDataMsg() : ComputeDPMEDataMsg
ComputeDPMEResultsMsg() : ComputeDPMEResultsMsg
ComputeEField() : ComputeEField
ComputeEwald() : ComputeEwald
ComputeExcls() : ComputeExcls
ComputeExt() : ComputeExt
computeExtMgr : BOCgroup
ComputeExtMgr() : ComputeExtMgr
ComputeFmmSerial() : ComputeFmmSerial
computeFmmSerialMgr : BOCgroup
ComputeFmmSerialMgr() : ComputeFmmSerialMgr
computeForce() : TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
ComputeFullDirect() : ComputeFullDirect
ComputeGBISser() : ComputeGBISser
computeGBISserMgr : BOCgroup
ComputeGBISserMgr() : ComputeGBISserMgr
ComputeGlobal : ComputeGlobal, HomePatch
ComputeGlobalDataMsg() : ComputeGlobalDataMsg
computeGlobalObject : ComputeMgr
ComputeGlobalResultsMsg() : ComputeGlobalResultsMsg
ComputeGridForce() : ComputeGridForce
ComputeHomePatch() : ComputeHomePatch
ComputeHomePatches() : ComputeHomePatches
ComputeHomeTuples() : ComputeHomeTuples< T, S, P >
ComputeImpropers() : ComputeImpropers
ComputeLCPO() : ComputeLCPO
computeLoad : processorInfo
computeMap : Node, LdbCoordinator
ComputeMap() : ComputeMap
computeMapData : ComputeMapMsg
computeMapFilename : SimParameters
computeMax() : Rebalancer
computeMgr : Node, BOCgroup
ComputeMgr : ComputeMgr, ComputeMap
ComputeMoa() : ComputeMoa
ComputeMsm() : ComputeMsm
computeMsmMgr : BOCgroup
ComputeMsmMgr() : ComputeMsmMgr
computeMsmMsaMgr : BOCgroup
ComputeMsmSerial() : ComputeMsmSerial
computeMsmSerialMgr : BOCgroup
ComputeMsmSerialMgr() : ComputeMsmSerialMgr
ComputeNonbondedCUDA() : ComputeNonbondedCUDA
ComputeNonbondedPair() : ComputeNonbondedPair
ComputeNonbondedSelf() : ComputeNonbondedSelf
ComputeNonbondedUtil() : ComputeNonbondedUtil
computePairHeap : Rebalancer
ComputePatch() : ComputePatch
ComputePatchPair() : ComputePatchPair
ComputePme : ComputePme, ComputePmeMgr
computePmeMgr : BOCgroup
ComputePmeMgr : ComputePmeMgr, NodePmeMgr
computeRecords : ComputeNonbondedCUDA
ComputeRestraints() : ComputeRestraints
computes : Rebalancer
ComputeSelfAngles() : ComputeSelfAngles
ComputeSelfAniso() : ComputeSelfAniso
ComputeSelfBonds() : ComputeSelfBonds
ComputeSelfCrossterms() : ComputeSelfCrossterms
ComputeSelfDihedrals() : ComputeSelfDihedrals
ComputeSelfExcls() : ComputeSelfExcls
computeSelfHeap : Rebalancer
ComputeSelfImpropers() : ComputeSelfImpropers
ComputeSelfThole() : ComputeSelfThole
ComputeSelfTuples() : ComputeSelfTuples< T, S, P >
computeSet : processorInfo
ComputeSphericalBC() : ComputeSphericalBC
ComputeStir() : ComputeStir
ComputeTclBC() : ComputeTclBC
ComputeThole() : ComputeThole
computeType : Compute
CONECT : PDBData
config : GlobalMasterEasy
config_s : colvarmodule
configFileInit() : NamdState
ConfigList() : ConfigList
configList : Node
configListInit() : NamdState
ConfigListNode() : ConfigList::ConfigListNode
conjugate() : colvarmodule::quaternion
consForce : Molecule
consForceFile : SimParameters
consForceIndexes : Molecule
consForceOn : SimParameters
consForceScaling : SimParameters
const_begin() : ResizeArray< Elem >, Array< Elem, Size >
const_end() : ResizeArray< Elem >, Array< Elem, Size >
const_iterator : ResizeArray< Elem >, Array< Elem, Size >
constant() : Matrix4
constant_pressure : OptPmeXPencil, OptPmePencilInitMsgData
consTorqueAxisFile : SimParameters
consTorqueFile : SimParameters
consTorqueGlobVal : SimParameters
consTorqueIndexes : Molecule
consTorqueOn : SimParameters
consTorqueParams : Molecule
consTorquePivotFile : SimParameters
consTorqueValFile : SimParameters
constraintExp : SimParameters
constraintScaling : SimParameters
constraintsOn : SimParameters
constrXOn : SimParameters
constrYOn : SimParameters
constrZOn : SimParameters
cont : GridforceFullBaseGrid
contributeToParent() : NodeProxyMgr
Controller : Controller, ScriptTcl, NamdState
ControllerBroadcasts() : ControllerBroadcasts
controllerExpected : LdbCoordinator
controllerReported : LdbCoordinator
controllerThread : LdbCoordinator
controlNumDegFreedom : Controller
controlPressure : Controller
controlPressure_nbond : Controller
controlPressure_normal : Controller
controlPressure_slow : Controller
cookie : MsmC1HermiteGridCutoff, MsmGridCutoff
coord : MoveAtomMsg, MsmSerialCoordMsg, msm::PatchData, GBISCoordMsg, FmmSerialCoordMsg, ExtCoordMsg
coordArray() : msm::PatchData
coordinate() : Output
coordinateNeeded() : Output
coordinates() : PDBAtom
coordnum() : colvar::coordnum
coords : Node
coordtmp : GlobalMasterIMD
coordtmpsize : GlobalMasterIMD
copy() : ResizeArray< Elem >, msm::Array< T >
copyPencils() : OptPmeCompute, ComputePmeMgr
copyResults() : ComputePmeMgr
core : DataMessage
corr_table : ComputeNonbondedUtil
correctMomentum() : Sequencer, Controller
cos_theta() : colvarmodule::rotation
cosAngles : SimParameters
cosine() : colvarmodule::quaternion
coulEnergy : GBISForceMsg
coulomb_radius_offset : SimParameters
count : PmeSharedUntransMsg, PmeSharedTransMsg
counter : TaggedMsg
cpuloads : LocalLBInfoMsg
cr_sortop() : cr_sortop
create() : colvar_grid< T >
create_hill() : colvarbias_meta
create_sorted_ids() : colvarmodule::atom_group
createAtomLists() : WorkDistrib
createCommands() : Measure
createComputes() : ComputeMgr
createHomePatch() : PatchMgr
createHomePatches() : WorkDistrib, ParallelIOMgr
createLoadBalancer() : LdbCoordinator
createPatchProxyListMsg() : PatchProxyListMsg
createProxies() : ProxyMgr
createProxy() : ProxyMgr
createProxyInfo() : NodeProxyMgr
createSpanningTree() : Rebalancer
createSTForHomePatches() : NodeProxyMgr
cross() : Vector, AVector
crossing_threshold : colvarmodule::rotation
crossterm_array : Parameters
crossterm_params() : crossterm_params
crossterm_type : crossterm
crosstermCnt : AtomSignature
CrosstermElem : CrosstermElem, Molecule
crosstermEnergyIndex : CrosstermElem
crosstermSigIndices : AtomSigInfo
crosstermSigs : AtomSignature
CRYST1 : PDBData
CUBIC : ComputeMsmMgr
cudaAtomList : ProxyDataMsg
cudaAtomPtr : Patch
curMFlopStep : Node
current_bin_scalar() : colvar_grid< T >
curTimeStep : Node
Cutcap : parm
cutoff : SimParameters, go_val, ComputeNonbondedUtil, GBISParamStruct
cutoff2 : ComputeNonbondedUtil
cutoff_3 : ComputeNonbondedUtil
cutoff_6 : ComputeNonbondedUtil
cv : colvar_grid< T >
cv_prec : colvarmodule
cv_traj_append : colvarmodule
cv_traj_freq : colvarmodule
cv_traj_name : colvarmodule
cv_traj_os : colvarmodule
cv_width : colvarmodule
cvc() : colvar::cvc
cvcs : colvar
cvm::atom : colvarproxy_namd
cycleBarrier() : Sequencer, Controller
cylindricalBCAxis : SimParameters
cylindricalBCexp1 : SimParameters
cylindricalBCexp2 : SimParameters
cylindricalBCk1 : SimParameters
cylindricalBCk2 : SimParameters
cylindricalBCl1 : SimParameters
cylindricalBCl2 : SimParameters
cylindricalBCOn : SimParameters
cylindricalBCr1 : SimParameters
cylindricalBCr2 : SimParameters
cylindricalCenter : SimParameters

- d -

d00 : CrosstermData
d01 : CrosstermData
d10 : CrosstermData
d11 : CrosstermData
d_stencil_1d() : ComputeMsmMgr
d_stencil_1d_c1hermite() : ComputeMsmMgr
daCutoffDist : SimParameters
daOffDist : SimParameters
daOnDist : SimParameters
data : msm::Grid< T >, ReductionSetData, ReductionSubmitMsg, Pointer, PAL, PatchGridElem, PencilElement, StreamMessage, OptPmePencil< T >, OptPmePencilInitMsg, DataMessage, ConfigList::ConfigListNode, StringList, PmePencil< T >, PmePencilInitMsg, colvar_grid< T >, CollectionMgr::CollectVectorSequence, CollectionMgr::CollectVectorInstance, CollectVectorVarMsg, DataStreamMsg, CollectionMaster::CollectVectorSequence, CollectionMaster::CollectVectorInstance, CollectVectorMsg, Array< Elem, Size >
data_begin_pos : colvarparse
data_end_pos : colvarparse
data_read : parm
data_size : CollectVectorMsg
data_types : ParseOptions::DataElement
DataElement() : ParseOptions::DataElement
DataExchanger() : DataExchanger
dataExchanger : BOCgroup
DataExchanger_SDAG_CODE : DataExchanger
dataQueue : ReductionSet
dataSize : ReductionSet, ReductionSubmitMsg, ReductionRegisterMsg
DataStatus : CollectVectorVarMsg
datastream() : datastream
dcdFilename : SimParameters
dcdFrequency : SimParameters
dcdUnitCell : SimParameters
dcos_theta_dq() : colvarmodule::rotation
deAssign() : Rebalancer
debug() : colvarmodule
debug_gradients() : colvar::cvc
debug_gradients_step_size : colvarmodule
decrease_depth() : colvarmodule
decrement() : ProxyUsage
decrSTLoad() : Rebalancer
dEdaSum : ProxyGBISP2ResultMsg, Patch, GBISParamStruct, ComputeNonbondedCUDA::patch_record
dEdaSumBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA::patch_record
dEdaSumBoxClosed() : Patch
dEdaSumComputeList : Patch
dEdaSumH : ComputeNonbondedCUDA
dEdaSumLen : ProxyGBISP2ResultMsg
default_border : GridforceFullMainGrid
default_coor : PDBAtom
default_occupancy : PDBAtom
default_residueseq : PDBAtom
default_serial : PDBAtom
default_temperaturefactor : PDBAtom
defined() : ParseOptions
del() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ResizeArray< Elem >
delete_alch_bonded() : Molecule
delete_hill() : colvarbias_meta
deleteCommands() : Measure
deleted : heapRecord
deleteMax() : maxHeap
deleteMin() : minHeap
delta : Lattice, four_body_consts, GBISParamStruct
delTmpPatchAtomsList() : PatchMap
density : NL_Msm_t
depositCombinedResultMsg() : ProxyPatch
depositCombinedResultRawMsg() : ProxyPatch
depositMigration() : HomePatch
depth : colvarmodule
dest : OptPmeSubComputeMsg
destElem : PmeUntransMsg, PmeTransMsg, PmeGridMsg
destNodeID : MigrationInfo
destPatchID : MigrationInfo, MigrateAtomsCombinedMsg, MigrateAtomsMsg
destPe : ProxyGBISP3DataMsg, ProxyGBISP2ResultMsg, ProxyGBISP2DataMsg, ProxyGBISP1ResultMsg
determinant() : colvarmodule::rmatrix
device_egrids : NL_Msm_t
device_qgrids : NL_Msm_t
dG : Controller
dhaCutoffAngle : SimParameters
dhaOffAngle : SimParameters
dhaOnAngle : SimParameters
dHdrPrefix : ProxyGBISP3DataMsg, Patch, GBISParamStruct, ComputeNonbondedCUDA::patch_record
dHdrPrefixBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA::patch_record
dHdrPrefixBoxClosed() : Patch
dHdrPrefixComputeList : Patch
dHdrPrefixLen : ProxyGBISP3DataMsg
diagonal() : Tensor
diagonalize_matrix() : colvarmodule::rotation
dielectric : SimParameters
dielectric_1 : ComputeNonbondedUtil
DihAt1 : parm
DihAt2 : parm
DihAt3 : parm
DihAt4 : parm
dihedPC() : colvar::dihedPC
dihedral : colvar::dihedral, lphost
dihedral_array : Parameters
dihedral_params() : dihedral_params
dihedral_type : dihedral
dihedralCnt : AtomSignature
DihedralElem : DihedralElem, Molecule
dihedralEnergyIndex : DihedralElem
dihedralOn : SimParameters
dihedralSigIndices : AtomSigInfo
dihedralSigs : AtomSignature
DihHAt1 : parm
DihHAt2 : parm
DihHAt3 : parm
DihHAt4 : parm
DihHNum : parm
DihNum : parm
dim : CrosstermValue
dim2 : PmeGrid
dim3 : PmeGrid
dimension : crossterm_params
disable() : colvar
dispersion : ComputeMsmMgr
disposeForces() : ParallelIOMgr, CollectionMaster
disposePositions() : ParallelIOMgr, CollectionMaster
disposeVelocities() : ParallelIOMgr, CollectionMaster
Dist() : AVector
dist2() : colvarvalue, colvarmodule::quaternion, colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
dist2_grad() : colvarvalue, colvarmodule::quaternion
dist2_lgrad() : colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
dist2_rgrad() : colvar::rmsd, colvar::spin_angle, colvar::tilt, colvar::orientation_angle, colvar::orientation, colvar::dihedPC, colvar::alpha_angles, colvar::h_bond, colvar::selfcoordnum, colvar::coordnum, colvar::dihedral, colvar::angle, colvar::eigenvector, colvar::inertia_z, colvar::inertia, colvar::gyration, colvar::distance_inv, colvar::distance_xy, colvar::distance_z, colvar::distance_dir, colvar::distance_vec, colvar::distance, colvar::cvc, colvar
dist_v : colvar::distance_z, colvar::distance
dist_v_ortho : colvar::distance_xy
distance : colvar::distance, lphost, bond_params
distance_dir() : colvar::distance_dir
distance_inv() : colvar::distance_inv
distance_vec() : colvar::distance_vec
distance_xy() : colvar::distance_xy
distance_z() : colvar::distance_z
distAttExp : SimParameters
distRepExp : SimParameters
distribute() : MigrateAtomsCombinedMsg
DistributeForce() : ARestraint
distributeHomePatches() : WorkDistrib
DistSqr() : AVector
dk : GridforceLiteGrid, GridforceFullBaseGrid
dk_hi : GridforceFullBaseGrid::GridIndices
dk_lo : GridforceFullBaseGrid::GridIndices
dk_nopad : GridforceFullBaseGrid
dL0_1 : colvarmodule::rotation
dL0_2 : colvarmodule::rotation
dM : OptPmeRealSpace
do_calc() : ComputeGridForce
doAtomMigration() : HomePatch
doEnergy : Flags, GBISParamStruct, ComputeNonbondedCUDA
dof_num : colvarvalue
doForce() : ComputeStir, ComputeSphericalBC, ComputeRestraints, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeLCPO, ComputeHomePatch, ComputeGridForce, ComputeEField, ComputeCylindricalBC, ComputeConsTorque, ComputeConsForce
doFullElectrostatics : Flags, GBISParamStruct
doGBIS : Flags, GBISParamStruct
doGroupSizeCheck() : HomePatch
doLCPO : Flags
doLoadTuples : ComputeHomeTuples< T, S, P >
doLoweAndersen : Flags, nonbonded
doMarginCheck() : HomePatch
doMolly : Flags
done() : MsmProfiler, MsmTimer
done_reading_files() : Parameters
done_reading_structure() : Parameters
doneCompute() : ComputeMsmMgr
doneSaveComputeMap() : WorkDistrib
doneUpdateLocalComputes() : ComputeMgr
doneVirialContrib() : ComputeMsmMgr
doNonbonded : Flags
donor : colvar::h_bond
doPairlistCheck() : HomePatch
doSlow : ComputeNonbondedCUDA, GBISCoordMsg
doSmoothing : GBISParamStruct
dot() : Vector, AVector
downstream() : PatchMap
downstreamNeighbors() : PatchMap
doWork() : OptPmeCompute, ComputeTclBC, ComputeSelfTuples< T, S, P >, ComputePme, ComputePatchPair, ComputePatch, ComputeNonbondedCUDA, ComputeMsmSerial, ComputeMsm, ComputeMoa, ComputeLCPO, ComputeHomeTuples< T, S, P >, ComputeHomePatch, ComputeGlobal, ComputeGBISser, ComputeFullDirect, ComputeFmmSerial, ComputeExt, ComputeEwald, Compute
doWorkOnPeer() : OptPmeCompute, OptPmeMgr
dQ0_1 : colvarmodule::rotation
dQ0_2 : colvarmodule::rotation
drudeBondConst : SimParameters
drudeBondLen : SimParameters
drudeBondTemp : Controller
drudeBondTempAvg : Controller
drudeComTemp : Controller
drudeComTempAvg : Controller
drudeDamping : SimParameters
drudeHardWallOn : SimParameters
drudeNbthole : ComputeNonbondedUtil
drudeNbtholeCut : SimParameters
drudeOn : SimParameters
drudeTemp : SimParameters
dS_1 : colvarmodule::rotation
dS_2 : colvarmodule::rotation
dspin_angle_dq() : colvarmodule::rotation
dsum : ClusterCoorMsg, ClusterCoorElem
dt : colvarproxy_namd, colvarproxy, colvarmodule, SimParameters
dudx : minpoint
dummy_atom_pos : colvarmodule::atom_group
dummy_pos : colvarparse
dummy_string : colvarparse
dump_fes : colvarbias_meta
dump_fes_save : colvarbias_meta
dump_replica_fes : colvarbias_meta
dump_tables() : HashPool< T >
dxdr1 : colvar::angle
dxdr3 : colvar::angle

- e -

e : GridforceLiteGrid, GridforceFullBaseGrid
Eangle : IMDEnergies
EarlyExit() : ARestraint
earlyExit() : Node
easy_calc() : GlobalMasterMisc, GlobalMasterEasy
easy_init() : GlobalMasterMisc, GlobalMasterEasy
Ebond : IMDEnergies
ed : colvar::h_bond, colvar::selfcoordnum, colvar::coordnum
Edihe : IMDEnergies
Eelec : IMDEnergies
eField : SimParameters
eFieldFreq : SimParameters
eFieldOn : SimParameters
eFieldPhase : SimParameters
eh : NL_Msm_t, MsmBlockKernel< Vtype, Mtype >, MsmGridCutoffKernel< Vtype, Mtype >, msm::PatchData
eh_c1hermite : msm::PatchData
eh_f : NL_Msm_t
ehBlockSend : MsmGridCutoffInitMsg
ehblockSend : MsmGridCutoffKernel< Vtype, Mtype >
ehfold : MsmGridCutoffKernel< Vtype, Mtype >
ehfull : MsmC1HermiteGridCutoff, MsmGridCutoff
ehProlongated : MsmBlockKernel< Vtype, Mtype >
eia : MsmGridCutoffKernel< Vtype, Mtype >
eib : MsmGridCutoffKernel< Vtype, Mtype >
eigenvec : colvar::eigenvector
eigenvec_invnorm2 : colvar::eigenvector
eigenvector() : colvar::eigenvector
eik : ComputeEwaldMsg
Eimpr : IMDEnergies
eja : MsmGridCutoffKernel< Vtype, Mtype >
ejb : MsmGridCutoffKernel< Vtype, Mtype >
eka : MsmGridCutoffKernel< Vtype, Mtype >
ekb : MsmGridCutoffKernel< Vtype, Mtype >
electEnergy : Controller
electEnergy_f : Controller
electEnergy_ti_1 : Controller
electEnergy_ti_2 : Controller
electEnergyIndex : ComputeNonbondedUtil, ExclElem
electEnergyIndex_s : ComputeNonbondedUtil
electEnergyIndex_ti_1 : ComputeNonbondedUtil
electEnergyIndex_ti_2 : ComputeNonbondedUtil
electEnergyPME_ti_1 : Controller
electEnergyPME_ti_2 : Controller
electEnergySlow : Controller
electEnergySlow_f : Controller
electEnergySlow_ti_1 : Controller
electEnergySlow_ti_2 : Controller
elem() : msm::Grid< T >, msm::GridFixed< T, N >, msm::Array< T >
element() : PDBAtom
en : colvar::h_bond, colvar::selfcoordnum, colvar::coordnum
en_prec : colvarmodule
en_width : colvarmodule
enable() : colvar
enableEarlyExit() : Node
enableExitScheduler() : Node
enableScriptBarrier() : Node
end : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ResizeArray< Elem >, MOStream, Array< Elem, Size >, OptPmeSubComputeMsg
END : PDBData
endd() : datastream
endi() : infostream
ENDMDL : PDBData
endPE : LocalLBInfoMsg
endtime : wkf_timer
endWork() : LdbCoordinator
energy : Output, colvarbias_meta::hill, MsmSerialForceMsg, msm::PatchData, FmmSerialForceMsg, ExtForceMsg
energy_difference() : colvarmodule, colvarbias_harmonic, colvarbias
energyNative : Molecule
energyNonnative : Molecule
eni : MsmGridCutoffKernel< Vtype, Mtype >
enj : MsmGridCutoffKernel< Vtype, Mtype >
enk : MsmGridCutoffKernel< Vtype, Mtype >
enqueue() : CollectionMaster::CollectVectorSequence
enqueueAngles() : WorkDistrib
enqueueAniso() : WorkDistrib
enqueueBonds() : WorkDistrib
enqueueCollections() : Controller
enqueueCrossterms() : WorkDistrib
enqueueCUDA() : WorkDistrib
enqueueCUDAP2() : WorkDistrib
enqueueCUDAP3() : WorkDistrib
enqueueDihedrals() : WorkDistrib
enqueueExcls() : WorkDistrib
enqueueForces() : CollectionMaster
enqueueImpropers() : WorkDistrib
enqueueLCPO() : WorkDistrib
enqueuePme() : WorkDistrib
enqueuePositions() : CollectionMaster
enqueueSelfA1() : WorkDistrib
enqueueSelfA2() : WorkDistrib
enqueueSelfA3() : WorkDistrib
enqueueSelfB1() : WorkDistrib
enqueueSelfB2() : WorkDistrib
enqueueSelfB3() : WorkDistrib
enqueueThole() : WorkDistrib
enqueueVelocities() : CollectionMaster
enqueueWork() : WorkDistrib, Compute
enqueueWorkA1() : WorkDistrib
enqueueWorkA2() : WorkDistrib
enqueueWorkA3() : WorkDistrib
enqueueWorkB1() : WorkDistrib
enqueueWorkB2() : WorkDistrib
enqueueWorkB3() : WorkDistrib
enqueueWorkC() : WorkDistrib
EntryGlob<Elem> : Entry< Elem >
Epot : IMDEnergies
epsilon : vdw_val, vdw_params, go_val
epsilon14 : vdw_val, vdw_params
epsilon_p : GBISParamStruct
epsilon_s : GBISParamStruct
epsilonRep : go_val
error_lside() : colvarvalue
error_message : ParseOptions::DataElement
error_rside() : colvarvalue
Etot : IMDEnergies
eval() : ScriptTcl
Evdw : IMDEnergies
evir : OptPmePencil< T >, PmePencil< T >, PmeUntransMsg, PmeGridMsg
ewaldcof : ComputeNonbondedUtil
ExclAt : parm
exclChecksumIndex : ComputeNonbondedUtil
ExclElem : ExclElem, Molecule
exclSigIdx : OutputAtomRecord::integerVals, BasicAtomInfo
ExclSigInfo() : ExclSigInfo
exclude : SimParameters
excludeFromPressure : SimParameters
Exclusion() : Exclusion
ExclusionCheck() : ExclusionCheck
ExclusionSignature() : ExclusionSignature
ExecuteMigrations() : LdbCoordinator
exists() : ParseOptions
exit() : colvarproxy_namd, colvarproxy, colvarmodule, BackEnd
ExitSchedOn() : BackEnd
exitScheduler() : Node
exp_a : go_val
exp_b : go_val
exp_dE_ByRT : Controller
exp_rep : go_val
expand_boundaries : colvar
expand_grids : colvarbias_meta
EXPDTA : PDBData
ExpectMigrate() : LdbCoordinator
exponent : colvar::distance_inv
ext_force_k : colvar
ext_gamma : colvar
ext_mass : colvar
ext_sigma : colvar
extCoordFilename : SimParameters
extendPtrs() : ComputeMap
extent() : msm::IndexRange
ExtForce() : ExtForce
extForceFilename : SimParameters
extForcesCommand : SimParameters
extForcesOn : SimParameters
extraBondsOn : SimParameters
extract() : msm::Grid< T >, msm::GridFixed< T, N >

- f -

f : Results, Patch, ComputeNonbondedCUDA::patch_record, LCPOAtom, TuplePatchElem, PatchElem, ComputeGlobalResultsMsg, ComputeConsForceMsg, colvar
f_0 : ComputeNonbondedWorkArrays
factor : GridforceFullBaseGrid
fast_table : ComputeNonbondedUtil
fatal_error() : colvarproxy_namd, colvarproxy, colvarmodule
fAtoms : GlobalMaster
fb : colvar
fdata : ParseOptions::DataElement, CollectionMgr::CollectVectorInstance, CollectVectorVarMsg, CollectionMaster::CollectVectorInstance, CollectVectorMsg
fdata_size : CollectVectorMsg
fdef : ParseOptions::DataElement
fdiff_velocity() : colvar
felec : NL_Msm_t
felec_f : NL_Msm_t
Fep_ElecOn : ComputeNonbondedUtil
Fep_WCA_dispOn : ComputeNonbondedUtil
Fep_WCA_repuOn : ComputeNonbondedUtil
Fep_Wham : ComputeNonbondedUtil
fepFile : Controller
FepNo : Controller
fepSum : Controller
ff : nonbonded
fflush_count : Controller
fft_init() : OptPmeXPencil, OptPmeYPencil, OptPmeZPencil, PmeXPencil, PmeYPencil, PmeZPencil
fftw_plan_lock : ComputePmeMgr
FFTWEstimate : SimParameters
FFTWPatient : SimParameters
FFTWUseWisdom : SimParameters
FFTWWisdomFile : SimParameters
FFTWWisdomString : SimParameters
fgrid : PmeGridMsg
fid : ComputeGlobalDataMsg
field() : PDBData
FIELDS : PDBData
file : FileStack
filename : GridforceLiteGrid, GridforceFullMainGrid, FileStack
fill_charges() : PmeRealSpace, OptPmeRealSpace
find() : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, IRSet, ResizeArray< Elem >, ConfigList
find_extremes() : PDB
find_key() : MGridforceParamsList
findOffset() : ExclusionSignature
finishWork() : ComputeNonbondedCUDA
first_timestep : colvarproxy_namd
firstAssignInRefine : Rebalancer
firstChild : DataExchanger
firstLdbStep : SimParameters, LdbCoordinator
firstResid : ResidueLookupElem
firstTime : GlobalMasterMisc
firstTimestep : SimParameters
firstwat() : parm
fit_gradients : colvarmodule::atom_group
fits_lattice() : GridforceGrid
fixCellDims : SimParameters
fixCellDimX : SimParameters
fixCellDimY : SimParameters
fixCellDimZ : SimParameters
fixed_axis : colvar::distance_z
fixedAtomsCntList : AtomsCntPerPatchMsg
fixedAtomsForces : SimParameters
fixedAtomsOn : SimParameters, ComputeNonbondedUtil
fixedPosition : FullAtom
fixglist : ComputeNonbondedWorkArrays
fj : colvar
flags : ProxyDataMsg, Patch, ExclusionCheck
flatindex() : msm::Grid< T >, msm::GridFixed< T, N >
flip() : OutputAtomRecord
flLen : ProxyCombinedResultRawMsg, ProxyResultVarsizeMsg
FLOAT : ParseOptions::DataElement
floatcomplex() : floatcomplex
FloatVector() : FloatVector
FloatVectorValid : CollectVectorVarMsg
FMAFFTBlock : SimParameters
FMAFFTOn : SimParameters
FMALevels : SimParameters
FMAMp : SimParameters
FMAOn : SimParameters
fmaTheta : SimParameters
FMMLevels : SimParameters
FMMOn : SimParameters
FMMPadding : SimParameters
foldfactor : msm::Map
FoldFactor() : msm::FoldFactor
footnote() : PDBAtom
force : Output, ExtForce, vmdforce, MsmSerialForceMsg, msm::PatchData, ComputeLCPO, GBISForceMsg, FmmSerialForceMsg, ExtForceMsg
force_k : colvarbias_harmonic
force_k_exp : colvarbias_harmonic
forceArr : ProxyCombinedResultRawMsg, ProxyResultVarsizeMsg
forceArray() : msm::PatchData
forceBox : Patch, ComputePatchPair, ComputePatch, ComputeNonbondedCUDA::patch_record, ComputeLCPO, TuplePatchElem, PatchElem
forceBoxClosed() : Patch
forceComputeList : Patch
forceconstant : angle_params, bond_params
forcedAtoms() : GlobalMaster
forceDcdFilename : SimParameters
forceDcdFrequency : SimParameters
forceIdBegin : GlobalMaster
forceIdEnd : GlobalMaster
forceList : ProxyCombinedResultMsg, ProxyResultMsg
forceNeeded() : Output
forces : ComputeNonbondedCUDA, ComputeDPMEResultsMsg
FORMUL : PDBData
forward_fft() : OptPmeXPencil, OptPmeYPencil, OptPmeZPencil, PmeXPencil, PmeYPencil, PmeZPencil
forward_plan : OptPmeXPencil, PmeXPencil
forward_subset_fft() : PmeYPencil
fptr : ParseOptions::DataElement
fr : colvar
free() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
freeBFactorData() : Molecule
freeEnergyOn : SimParameters
freeMolSpace() : ParallelIOMgr
freeOccupancyData() : Molecule
from : MovePatchAtomsMsg, LdbMigrateMsg
fromNodeID : MovePatchesMsg, MigrateAtomsCombinedMsg, MigrateAtomsMsg
fromRaw() : ProxyCombinedResultMsg
fSet : OutputAtomRecord
fsMax : SimParameters, GBISParamStruct
ft : colvar::cvc, colvar
ft_reported : colvar
FTNOTE : PDBData
full_table : ComputeNonbondedUtil
fullDirectOn : SimParameters
fullElectEnergyIndex : ComputeNonbondedUtil, ExclElem
fullElectEnergyIndex_s : ComputeNonbondedUtil
fullElectEnergyIndex_ti_1 : ComputeNonbondedUtil
fullElectEnergyIndex_ti_2 : ComputeNonbondedUtil
fullElectFrequency : SimParameters
fullElectVirialIndex : ComputeNonbondedUtil
fullExclCnt : ExclusionSignature
fullExclOffset : ExclSigInfo
fullf : nonbonded
fullf_0 : ComputeNonbondedWorkArrays
fullOffset : ExclusionSignature
function_type : colvar::cvc
fwdSharedTrans() : ComputePmeMgr
fwdSharedUntrans() : ComputePmeMgr

- g -

gA : Molecule, GroGaussPair
gamma : GBISParamStruct
gap : GridforceFullBaseGrid
gapinv : GridforceFullBaseGrid
gather_coordinates() : IMDOutput
gather_energies() : IMDOutput
gaussian() : Random
gaussian_vector() : Random
gbInterEnergy : GBISParamStruct, GBISForceMsg
gbis_beta : SimParameters
gbis_delta : SimParameters
gbis_gamma : SimParameters
gbisComputeAfterP1() : HomePatch
gbisComputeAfterP2() : HomePatch
GBISOn : SimParameters
gbisP2PatchReady() : Compute
gbisP2Ready() : Patch, HomePatch
gbisP3PatchReady() : Compute
gbisP3Ready() : Patch, HomePatch
gbisParams : ComputeNonbondedSelf, ComputeNonbondedPair
gbisPhase : GBISParamStruct, Compute
gbisPhasePriority : Compute
GBISserOn : SimParameters
gbisStepPairlists : GBISParamStruct, ComputeNonbondedSelf, ComputeNonbondedPair
gbqs : MoaData
gbSelfEnergy : GBISParamStruct, GBISForceMsg
gc : msm::Map, NL_Msm_t
gc_c1hermite : msm::Map
gc_c1hermite_elem_accum() : ComputeMsmMgr
gc_f : NL_Msm_t
gcom : ComputeGlobalDataMsg
gcutAssign : ComputeMsmMgr
gdata : GridMsg
genclose() : parm
genCompressedPsf : SimParameters
generation : GridforceFullBaseGrid
GenericAngle() : GenericAngle
GenericAtom() : GenericAtom
GenericBond() : GenericBond
GenericDihedral() : GenericDihedral
GenericMol() : GenericMol
genopen() : parm
get() : ParseOptions, parm, MIStream, MsmC1HermiteGridCutoffSetupMsg, MsmGridCutoffSetupMsg, MsmC1HermiteGridCutoffProxyMsg, MsmGridCutoffProxyMsg, MsmC1HermiteBlockProxyMsg, MsmBlockProxyMsg, GridMsg, SimpleBroadcastObject< T >
get_acceptor() : Molecule
get_all_gridvals() : GridforceLiteGrid, GridforceFullMainGrid, GridforceGrid
get_all_positions() : PDB
get_angle() : Molecule
get_angle_params() : Parameters
get_angles_for_atom() : Molecule
get_atom_from_index_in_residue() : Molecule
get_atom_from_name() : Molecule
get_atomtype() : Molecule
get_bond() : Molecule
get_bond_params() : Parameters
get_bonds_for_atom() : Molecule
get_border() : GridforceFullSubGrid, GridforceFullMainGrid, GridforceFullBaseGrid
get_center() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_cluster() : Molecule
get_clusterSize() : Molecule
get_colvars_index() : colvar_grid< T >
get_cons_params() : Molecule
get_constorque_params() : Molecule
get_corner() : GridforceGrid
get_crossterm() : Molecule
get_crossterms_for_atom() : Molecule
get_dihedral() : Molecule
get_dihedral_multiplicity() : Parameters
get_dihedral_params() : Parameters
get_dihedrals_for_atom() : Molecule
get_donor() : Molecule
Get_dU_dLambda() : AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, AForcingPosRestraint, ARestraint
get_e() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_excl_check_for_atom() : Molecule
get_exclusion() : Molecule
get_exclusions_for_atom() : Molecule
get_extremes() : PDB
get_fep_type() : Molecule
get_first() : MGridforceParamsList
get_full_exclusions_for_atom() : Molecule
get_go_cutoff() : Molecule
get_go_epsilon() : Molecule
get_go_epsilonRep() : Molecule
get_go_exp_a() : Molecule
get_go_exp_b() : Molecule
get_go_exp_rep() : Molecule
get_go_force() : Molecule
get_go_force2() : Molecule
get_go_force_new() : Molecule
get_go_sigmaRep() : Molecule
get_grid() : GridforceLiteGrid, GridforceFullBaseGrid
get_grid_d() : GridforceLiteGrid, GridforceFullBaseGrid
get_grid_type() : GridforceGrid
get_gridfrc_grid() : Molecule
get_gridfrc_params() : Molecule
get_gro_force() : Molecule
get_gro_force2() : Molecule
get_groupSize() : Molecule
get_improper() : Molecule
get_improper_multiplicity() : Parameters
get_improper_params() : Parameters
get_impropers_for_atom() : Molecule
get_inds() : GridforceLiteGrid, GridforceFullBaseGrid
get_int_table_type() : Parameters
get_inv() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_k0() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_k1() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_k2() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_lphost() : Molecule
get_mod_exclusions_for_atom() : Molecule
get_mother_atom() : Molecule
get_movdrag_params() : Molecule
get_num_vdw_params() : Parameters
get_origin() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_position_for_atom() : PDB
get_residue_size() : Molecule
get_rotdrag_params() : Molecule
get_scale() : GridforceLiteGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid
get_stir_refPos() : Molecule
get_stir_startTheta() : Molecule
get_table() : LJTable
get_table_dim() : LJTable
get_table_pair_params() : Parameters
get_total_grids() : GridforceLiteGrid, GridforceFullMainGrid, GridforceGrid
get_vdw_pair_params() : Parameters
get_vdw_params() : Parameters
get_vector() : colvarmodule::quaternion
get_vmd_forces() : GlobalMasterIMD
GetAccumulation() : ALambdaManager, ALambdaControl
getAllAcceptors() : Molecule
getAllAngles() : Molecule
getAllBonds() : Molecule
getAllCrossterms() : Molecule
getAllDihedrals() : Molecule
getAllDonors() : Molecule
getAllImpropers() : Molecule
getAllLphosts() : Molecule
getANewMsg() : ProxyNodeAwareSpanningTreeMsg, ProxyResultVarsizeMsg
GetAngle() : ARestraint
getAngle() : GromacsTopFile, GenericMol
getAngleParams() : GromacsTopFile
GetAngleTarget() : AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AnAngleRestraint
getAtom() : GromacsTopFile, GenericMol
GetAtomAlpha() : Molecule
getAtomi() : GenericDihedral, GenericAngle, GenericBond
getAtomID() : GlobalMasterFreeEnergy, GlobalMasterEasy
getAtomIdBegin() : GlobalMaster
getAtomIdEnd() : GlobalMaster
getAtomj() : GenericDihedral, GenericAngle, GenericBond
getAtomk() : GenericDihedral, GenericAngle
getAtoml() : GenericDihedral
getAtomList() : HomePatch
getAtomName() : GenericAtom
getAtomNames() : Molecule
getAtomParams() : GromacsTopFile
getAtomPositionBegin() : GlobalMaster
getAtoms() : Molecule
getAtomSegResInfo() : Molecule
getBFactorData() : Molecule
getBond() : GromacsTopFile, GenericMol
getBondParams() : GromacsTopFile
GetBound() : ABoundAngleRestraint, ABoundDistRestraint, ABoundPosRestraint
getbuf() : BroadcastMgr
getCharge() : GenericAtom
getCompAtomExtInfo() : Patch
getCudaAtomList() : Patch
getData() : ReductionSet, PressureProfileReduction
GetDihe() : ARestraint
getDihedral() : GromacsTopFile, GenericMol
getDihedralParams() : GromacsTopFile
GetDiheTarget1() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, ADiheRestraint
GetDiheTarget2() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, ADiheRestraint
GetDistance() : AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, APosRestraint
GetDistTarget() : AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, ADistRestraint
GetE() : ADiheRestraint, AnAngleRestraint, ADistRestraint, APosRestraint
GetEnergy() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, ARestraint
getExclusions() : GromacsTopFile
getFlags() : ComputeHomePatches
getForceIdBegin() : GlobalMaster
getForceIdEnd() : GlobalMaster
getGBISPhase() : Compute
GetGrad() : ADiheRestraint, AnAngleRestraint, ADistRestraint, APosRestraint
GetGradient() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, ARestraint
getGroupMassBegin() : GlobalMaster
getGroupMassEnd() : GlobalMaster
getGroupPositionBegin() : GlobalMaster
getGroupPositionEnd() : GlobalMaster
getIndex() : DihedralTable, AngleTable, BondTable
getIndexValue() : Pairlists
GetIntegration() : ALambdaManager, ALambdaControl
GetIntervalAngle() : ABoundDiheRestraint
GetKf() : ARestraint
GetLambdaKf() : ARestraint, ALambdaControl
GetLambdaRef() : ARestraint, ALambdaControl
GetLambdas() : ALambdaManager
getLastAtomsForcedBegin() : GlobalMaster
getLastAtomsForcedEnd() : GlobalMaster
getLastForcesBegin() : GlobalMaster
getLcpoParamType() : Molecule
getline_nocomments() : colvarparse
getLocalPatchMap() : NodeProxyMgr
getLocalProxyMgr() : NodeProxyMgr
GetLowerAngle() : ABoundDiheRestraint
getMass() : GenericAtom, GlobalMasterFreeEnergy, GlobalMasterEasy
getMasterChareID() : CollectionMgr
getMasterNode() : ComputeEwald
getMessage() : Communicate
getMol() : MolInst
getMoleculePointers() : TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
getName() : GenericMol
getNewArray() : ObjectArena< Type >
getNum() : MolInst
GetNum_dU_dLambda() : ALambdaManager, ALambdaControl
GetNumAccumStepsSoFar() : ALambdaManager, ALambdaControl
getNumAngleParams() : GromacsTopFile
getNumAngles() : GromacsTopFile, MolInst, GenericMol
getNumAtomParams() : GromacsTopFile
getNumAtoms() : Patch, GromacsTopFile, MolInst, GenericMol, GlobalMasterFreeEnergy, GlobalMasterEasy
getNumBondParams() : GromacsTopFile
getNumBonds() : GromacsTopFile, MolInst, GenericMol
getNumComputes() : Patch
getNumDihedralParams() : GromacsTopFile
getNumDihedrals() : GromacsTopFile, MolInst, GenericMol
getNumExclusions() : GromacsTopFile
getNumFixedAtoms() : Patch
getNumGaussPair() : GromacsTopFile
GetNumGroups() : ARestraint
GetNumInGroup() : AGroup
getNumLJPair() : GromacsTopFile
getNumLocalAtoms() : OptPmeCompute
GetNumObjects() : ALambdaManager
getNumOutputProcs() : ParallelIOMgr
getNumPair() : GromacsTopFile
getNumPatches() : Compute
getNumRes() : MolInst, GenericMol
GetNumRestraints() : ARestraintManager
GetNumSteps() : ALambdaControl
GetNumStepsSoFar() : ALambdaManager, ALambdaControl
getNumStepsToRun() : LdbCoordinator
getOccupancyData() : Molecule
GetPaddedTaskStr() : ALambdaControl
getPairGaussArrays2() : GromacsTopFile, PairTable
getPairLJArrays2() : GromacsTopFile, PairTable
getParameterPointers() : TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
getParams() : VDWTable, DihedralTable, AngleTable, BondTable, AtomTable
getPatchesInOctet() : PatchMap
getPatchID() : Patch
getPatchProxyInfo() : NodeProxyMgr
getPlugin() : PluginIOMgr
getPosition() : GlobalMasterFreeEnergy, GlobalMasterEasy
GetPosTarget() : AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, APosRestraint
getPtree() : ProxyMgr
getRecvSpanning() : ProxyMgr
GetRefAngle() : AFixedDiheRestraint, ABoundAngleRestraint, AFixedAngleRestraint
GetRefDist() : ABoundDistRestraint, AFixedDistRestraint, ABoundPosRestraint
GetRefPos() : ABoundPosRestraint, AFixedPosRestraint
getResNum() : GenericAtom
getResType() : GenericAtom
getScript() : Node
getSendSpanning() : ProxyMgr
getSize() : Pairlists, LCPONeighborList
getSpanningTreeChild() : ProxyPatch
getSpanningTreeChildPtr() : ProxyPatch
getSpanningTreeNChild() : ProxyPatch
getSpanningTreeParent() : ProxyPatch
GetStartAngle() : AForcingDiheRestraint, AForcingAngleRestraint
GetStartDist() : AForcingDistRestraint
GetStartPos() : AForcingPosRestraint
GetStopAngle() : AForcingDiheRestraint, AForcingAngleRestraint
GetStopDist() : AForcingDistRestraint
GetStopPos() : AForcingPosRestraint
GetStr() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, AForcingAngleRestraint, ABoundAngleRestraint, AFixedAngleRestraint, AForcingDistRestraint, ABoundDistRestraint, AFixedDistRestraint, AForcingPosRestraint, ABoundPosRestraint, AFixedPosRestraint, ARestraint
getSystemName() : GromacsTopFile
GetTask() : ALambdaControl
GetTaskStr() : ALambdaControl
getTmpPatchAtomsList() : PatchMap
getTotalForce() : GlobalMaster
GetTotalNumSteps() : ALambdaManager
getTupleInfo() : TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
getType() : AtomTable, GenericAtom, GenericDihedral, GenericAngle, GenericBond
getTypeNum() : GenericAtom
GetUpperAngle() : ABoundDiheRestraint
getVal() : ProxyUsage, HashPoolAdaptorT< T >
getVDWParams() : GromacsTopFile
gforce : ComputeGlobalResultsMsg
giSigma1 : Molecule, GroGaussPair
giSigma2 : Molecule, GroGaussPair
globalForcesOn : SimParameters
GlobalMaster() : GlobalMaster
GlobalMasterEasy() : GlobalMasterEasy
GlobalMasterFreeEnergy() : GlobalMasterFreeEnergy
GlobalMasterIMD() : GlobalMasterIMD
GlobalMasterMisc() : GlobalMasterMisc
GlobalMasterServer() : GlobalMasterServer
GlobalMasterSMD() : GlobalMasterSMD
GlobalMasterSymmetry() : GlobalMasterSymmetry
GlobalMasterTcl : GlobalMasterTcl, ScriptTcl
GlobalMasterTMD() : GlobalMasterTMD
globalOn : SimParameters
globHead : UniqueSetRaw< Elem >
gMu1 : Molecule, GroGaussPair
gMu2 : Molecule, GroGaussPair
go_array : Molecule
go_indices : Molecule
go_restricted() : Molecule
goCoordinates : SimParameters, Molecule
goForcesOn : SimParameters, ComputeNonbondedUtil
goGroPair : SimParameters, ComputeNonbondedUtil
goIndxA : go_pair
goIndxB : go_pair
goIndxLJA : Molecule
goIndxLJB : Molecule
goInit() : Molecule
goMethod : SimParameters, ComputeNonbondedUtil
goNativeEnergy : Controller
goNativeEnergyIndex : ComputeNonbondedUtil
goNonnativeEnergy : Controller
goNonnativeEnergyIndex : ComputeNonbondedUtil
goNumLJPair : Molecule
goodglist : ComputeNonbondedWorkArrays
goParameters : SimParameters
goPDB : Molecule
goResidIndices : Molecule
goResids : Molecule
goSigmaIndices : Molecule
goSigmaPairA : Molecule
goSigmaPairB : Molecule
goSigmas : Molecule
goTotalEnergy : Controller
gotoUsed() : UniqueSetIter< T >
goWithinCutoff : Molecule
GPID : InputAtom, HydrogenGroupID, OutputAtomRecord::integerVals
gpro_c1hermite : msm::Map
grad : colvarmodule::atom
gradient_finite_diff() : colvar_grid_scalar
gradU() : ADiheRestraint
gRepulsive : Molecule, GroGaussPair
gres_c1hermite : msm::Map
grespro : msm::Map
Grid() : msm::Grid< T >
grid : GridforceLiteGrid, GridforceFullBaseGrid, OptPmePencilInitMsgData, PmePencilInitMsgData
Grid<T> : msm::GridFixed< T, N >
grid_index() : GridforceLiteGrid, GridforceFullBaseGrid
gridCalc1() : ComputePmeMgr
gridCalc2() : ComputePmeMgr
gridCalc2R() : ComputePmeMgr
gridCalc3() : ComputePmeMgr
GRIDCUTOFF : MsmTimer
gridCutoff() : MsmC1HermiteBlock, MsmBlock
GridFixed() : msm::GridFixed< T, N >
gridforceCol : MGridforceParams
gridforceCont : MGridforceParams
gridforceContA1 : SimParameters
gridforceContA2 : SimParameters
gridforceContA3 : SimParameters
gridforceFile : MGridforceParams
GridforceFullBaseGrid : GridforceFullBaseGrid, GridforceFullSubGrid, GridforceFullMainGrid
GridforceFullMainGrid : GridforceFullMainGrid, GridforceFullSubGrid, GridforceFullBaseGrid
GridforceFullSubGrid : GridforceFullSubGrid, GridforceFullMainGrid, GridforceFullBaseGrid
GridforceGridType : GridforceGrid
GridforceGridTypeFull : GridforceGrid
GridforceGridTypeLite : GridforceGrid
GridforceGridTypeUndefined : GridforceGrid
gridforceKey : MGridforceParams
gridforceLite : SimParameters, MGridforceParams
GridforceLiteGrid() : GridforceLiteGrid
gridforceOn : SimParameters
gridforceQcol : MGridforceParams
gridforceScale : SimParameters, MGridforceParams
gridforceVfile : MGridforceParams
gridforceVOffset : SimParameters, MGridforceParams
gridforceVolts : SimParameters, MGridforceParams
gridrange : msm::Map
grids_freq : colvarbias_meta
gridScalingFactor : ComputeMsmMgr
gridsize_a() : PatchMap
gridsize_b() : PatchMap
gridsize_c() : PatchMap
gridspacing : NL_Msm_t, ComputeMsmMgr
GroGaussCompare() : PairTable
groGaussEnergy : Controller
groGaussEnergyIndex : ComputeNonbondedUtil
GroLJCompare() : PairTable
groLJEnergy : Controller
groLJEnergyIndex : ComputeNonbondedUtil
gromacsOn : SimParameters
GromacsTopFile() : GromacsTopFile
group : GroupInitMsg
group1 : colvar::dihedral, colvar::angle, colvar::distance
group2 : colvar::dihedral, colvar::angle, colvar::distance
group3 : colvar::dihedral, colvar::angle
group4 : colvar::dihedral
groupFixed : CompAtomExt
groupForces() : GlobalMaster
grouplist : ComputeNonbondedWorkArrays
groupMasses : GlobalMaster
groupplcutoff : nonbonded
groupPositionBegin : GlobalMaster
groupPositionEnd : GlobalMaster
groupPressure : Controller
groupPressure_avg : Controller
groupPressure_nbond : Controller
groupPressure_normal : Controller
groupPressure_slow : Controller
groupPressure_tavg : Controller
grpForces : GlobalMaster
gvc : msm::Map
gvc_c1hermite : msm::Map
gvsum : ComputeMsmMgr
gx : NL_Msm_t
gx_f : NL_Msm_t
gy : NL_Msm_t
gy_f : NL_Msm_t
gyration() : colvar::gyration
gz : NL_Msm_t
gz_f : NL_Msm_t
gzero : NL_Msm_t, ComputeMsmMgr
gzero_f : NL_Msm_t

- h -

h_bond() : colvar::h_bond
haAngleExp : SimParameters
handle : LdbMigrateMsg, OptPmePencil< T >, computeInfo
hard_lower_boundaries : colvar_grid< T >
hard_lower_boundary : colvar
hard_upper_boundaries : colvar_grid< T >
hard_upper_boundary : colvar
hardWallDrude() : Sequencer, HomePatch
has_data : colvar_grid< T >, colvarbias
has_default : ParseOptions::DataElement
has_evir : PmeUntransMsg
has_parent_data : colvar_grid< T >
HAS_PROCESSED : CollectionMaster
hasData : PmePencil< T >, PmeTransMsg, PmeGridMsg
hasElements() : IRSet
hash() : ExclusionSignature, TupleSignature, Exclusion, ProxyUsageKey, ProxyElem, ClusterCoorElem, ClusterElem, TholeElem, ExclElem, ImproperElem, TuplePatchElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem, HashPoolAdaptorT< T >, HashReal, HashString, ExclSigInfo, AtomSigInfo, BOID, TaggedMsg, BroadcastClientElem
HashPoolAdaptorT() : HashPoolAdaptorT< T >
HashReal() : HashReal
hasLB : MoaData
hasLQ : MoaData
hasLS : MoaData
hasNewAtoms() : Patch
hasPatchZero : ComputeHomePatches
hb : colvar::alpha_angles
HB12 : parm
HB6 : parm
hb_coeff : colvar::alpha_angles
head() : ConfigList
header : StreamMessage
HEADER : PDBData
HELIX : PDBData
HET : PDBData
HETATM : PDBData
hgroupCutoff : SimParameters
high : netint
highest : netint
hill() : colvarbias_meta::hill
hill_iter : colvarbias_meta
hill_value : colvarbias_meta::hill
hill_weight : colvarbias_meta
hill_width : colvarbias_meta
hills : colvarbias_meta
hills_energy : colvarbias_meta
hills_energy_gradients : colvarbias_meta
hills_off_grid : colvarbias_meta
hills_traj_os : colvarbias_meta
holdComputes() : Sync
homePatch : PatchMgr, PatchMap, ComputeHomePatch
HomePatch : Sequencer
HomePatchElem() : HomePatchElem
homePatchIDList() : PatchMap
homePatchList() : PatchMap
host_egrids : NL_Msm_t
host_lfac : NL_Msm_t
host_qgrids : NL_Msm_t
host_sinfo : NL_Msm_t
host_wt : NL_Msm_t
hostedPatches : ComputeNonbondedCUDA
hostPe : ComputeNonbondedCUDA::patch_record
htable : ProxyUsage
hu : ComputeMsmMgr
hufx : ComputeMsmMgr
hufy : ComputeMsmMgr
hufz : ComputeMsmMgr
hv : ComputeMsmMgr
hvfx : ComputeMsmMgr
hvfy : ComputeMsmMgr
hvfz : ComputeMsmMgr
hw : ComputeMsmMgr
hwfx : ComputeMsmMgr
hwfy : ComputeMsmMgr
hwfz : ComputeMsmMgr
hx : NL_Msm_t
hx_f : NL_Msm_t
hxlen : ComputeMsmMgr
hxlen_1 : ComputeMsmMgr
hy : NL_Msm_t
hy_f : NL_Msm_t
hybridGroupSize : SimParameters
hydList : InputAtom
HydrogenBonds : SimParameters
hydrogenGroup : Molecule
HydrogenGroupID() : HydrogenGroupID
hydrogenGroupSize : CompAtom
hydrogenList : AtomCstInfo, atom_constants, OutputAtomRecord::integerVals
hylen : ComputeMsmMgr
hylen_1 : ComputeMsmMgr
hz : NL_Msm_t
hz_f : NL_Msm_t
hzlen : ComputeMsmMgr
hzlen_1 : ComputeMsmMgr

- i -

i : doublecomplex, Transform, msm::Ivec, netint, ijpair, floatcomplex
ia() : msm::IndexRange
Iac : parm
ib : msm::IndexRange, PencilElement
Iblo : parm
id : Iterator, CompAtomExt, msm::AtomCoord, ComputeMsmSerialAtom, ComputeGBISAtom, ComputeFmmSerialAtom, ComputeExtAtom, colvarbias, colvarmodule::atom, BOID, BroadcastClient
Id : InfoRecord
idata : ParseOptions::DataElement
idef : ParseOptions::DataElement
identity() : Tensor, Matrix4Symmetry, Matrix4, Matrix4TMD
idleTime : processorInfo
idnum : GridMsg
IfBox : parm
IfCap : parm
ignoreMass : SimParameters
ijpair() : ijpair
imd : Node
IMDfreq : SimParameters
IMDignore : SimParameters, GlobalMasterIMD
IMDon : SimParameters
IMDOutput : IMDOutput, GlobalMasterIMD
IMDport : SimParameters
IMDwait : SimParameters, GlobalMasterIMD
improper_array : Parameters
improper_type : improper
improperCnt : AtomSignature
ImproperElem : ImproperElem, Molecule
improperEnergyIndex : ImproperElem
improperSigIndices : AtomSigInfo
improperSigs : AtomSignature
imsg : OptPmePencil< T >, PmePencil< T >
imsgb : PmePencil< T >
IN_PROCESS : CollectionMaster
IncCurrStep() : ALambdaManager, ALambdaControl
incr() : colvar_grid< T >
incr_count() : colvar_grid_count
increase_depth() : colvarmodule
increment() : ProxyUsage
incrSTLoad() : Rebalancer
ind1 : indexed_table_pair, nbthole_pair_value, indexed_nbthole_pair, indexed_vdw_pair
ind2 : indexed_table_pair, nbthole_pair_value, indexed_nbthole_pair, indexed_vdw_pair
index : SortedArray< Elem >, Lattice, ParseOptions::DataElement, nbthole_pair_params, vdw_params, crossterm_params, improper_params, dihedral_params, angle_params, bond_params, __sort_entry, LocalID, StreamMessage, position_index, vmdforce, WorkIndex, NonbondedCUDASlaveMsg, colvarmodule::atom
index_a() : PatchMap
index_b() : PatchMap
index_c() : PatchMap
index_for_key() : MGridforceParamsList
index_ok() : colvar_grid< T >
indexGridCutoff : msm::BlockDiagram
IndexOffset : ComputeMsmMgr
IndexRange() : msm::IndexRange
indexRangeOfBlock() : msm::Map
indexRangeOfBlockFold() : msm::Map
inds2 : GridforceFullBaseGrid::GridIndices
indxGaussA : Molecule, GroGaussPair
indxGaussB : Molecule, GroGaussPair
indxLJA : Molecule, GroLJPair
indxLJB : Molecule, GroLJPair
inertia() : colvar::inertia
inertia_z() : colvar::inertia_z
info : listNode, heapRecord
infostream() : infostream
Init() : ALambdaControl
init() : SortableResizeArray< Elem >, Random, msm::Grid< T >, msm::GridFixed< T, N >, msm::PriorityQueue< T >, MsmBlockKernel< Vtype, Mtype >, MsmC1HermiteGridCutoff, MsmGridCutoff, MsmGridCutoffKernel< Vtype, Mtype >, msm::PatchData, BackEnd
init_biases() : colvarmodule
init_colvars() : colvarmodule
init_namd_atom() : colvarproxy_namd
initdata : OptPmePencil< T >, PmePencil< T >
initialize() : ParallelIOMgr, OptPmeMgr, Molecule, LdbCoordinator, GridforceLiteGrid, GridforceFullSubGrid, GridforceFullMainGrid, GridforceGrid, OptPmePencilMapZ, OptPmePencilMapY, OptPmePencilMapX, ComputeSelfTuples< T, S, P >, ComputePme, NodePmeMgr, ComputePmeMgr, ComputePatchPair, ComputePatch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeMsmMgr, ComputeLCPO, ComputeHomeTuples< T, S, P >, ComputeHomePatches, ComputeHomePatch, Compute
initialize_computes() : ComputePmeMgr
initialize_config_data() : SimParameters
initialize_manytomany() : OptPmeXPencil
initialize_pencils() : OptPmeMgr, ComputePmeMgr
initialTemp : SimParameters
InitProxyUsage() : Rebalancer
initPtrs() : ComputeMap
initRSS : Node
initTmpPatchAtomsList() : PatchMap
initVirialContrib() : ComputeMsmMgr
initVM : Node
inMigration : HomePatch
inner() : colvarmodule::quaternion
inner_opt() : colvarvalue
input_prefix : colvarproxy_namd, colvarproxy, colvarmodule
input_prefix_str : colvarproxy_namd
insert() : UniqueSortedArray< Elem >, SortedArray< Elem >, IRSet, ResizeArray< Elem >, msm::PriorityQueue< T >, maxHeap, minHeap
insertioncode() : PDBAtom
Instance() : PatchMap, ComputeMap, AtomMap
INT : ParseOptions::DataElement
Int2() : Int2
Int3() : Int3
integer() : Random
integrate() : Sequencer, Controller
Integrate_MCTI() : ALambdaManager, ALambdaControl
integrateClusterSize() : ParallelIOMgr
integrateMigratedAtoms() : ParallelIOMgr
INTERP : MsmTimer
interpolation() : msm::PatchData
interpolationC1Hermite() : msm::PatchData
intRad : Patch, GBISParamStruct, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA::patch_record
intRadBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA::patch_record
intRadBoxClosed() : Patch
intRadComputeList : Patch
intRadList : ProxyDataMsg
inv : GridforceLiteGrid, GridforceFullBaseGrid
invalidPatch : ComputeLCPO
inverse() : Matrix4, colvarvalue, colvarmodule::rotation
ioMgr : BOCgroup
ion_concentration : SimParameters
Ipatm : parm
Ipres : parm
iptr : ParseOptions::DataElement
Iptres : parm
IRSet() : IRSet
is_atom_constorqued() : Molecule
is_atom_constrained() : Molecule
is_atom_exPressure() : Molecule
is_atom_fixed() : Molecule
is_atom_gridforced() : Molecule
is_atom_movdragged() : Molecule
is_atom_rotdragged() : Molecule
is_atom_stirred() : Molecule
is_defined : ParseOptions::DataElement
is_drude() : Molecule
is_drude_psf : Molecule
is_group_fixed() : Molecule
is_hydrogen() : Molecule
is_hydrogenGroupParent() : Molecule
is_lonepairs_psf : Molecule
is_lp() : Molecule
is_optional : ParseOptions::DataElement
is_oxygen() : Molecule
is_scalar() : colvarvalue
is_water() : Molecule
IsActive() : ALambdaControl
isActive : PencilElement
isAvailableOn() : Rebalancer
isBasePatch : ComputeHomeTuples< T, S, P >
isBFactorValid : Molecule
isEmpty() : TupleSignature
IsEndOf_MCTI() : ALambdaManager, ALambdaControl
IsEndOf_MCTI_Step() : ALambdaManager, ALambdaControl
iSet : OutputAtomRecord
IsFirstStep() : ALambdaManager, ALambdaControl
isfold : MsmGridCutoffKernel< Vtype, Mtype >
isForceNonZero : ProxyCombinedResultRawMsg
IsForcing() : AForcingDiheRestraint, AForcingAngleRestraint, AForcingDistRestraint, AForcingPosRestraint, ARestraint
isGP : InputAtom, HydrogenGroupID
isLocal : ComputeNonbondedCUDA::patch_record
isMP : InputAtom, HydrogenGroupID
isOccupancyValid : Molecule
isOpen() : OwnerBox< Owner, Data >
isOutputProcessor() : ParallelIOMgr
isPmeProcessor() : ComputePmeMgr
ispu : ComputeMsmMgr
ispv : ComputeMsmMgr
ispw : ComputeMsmMgr
ispx : msm::Map
ispy : msm::Map
ispz : msm::Map
isReal : TupleSignature
isRecvSpanningTreeOn() : SimParameters
isRecvSpanningTreeUnset() : SimParameters
isSendSpanningTreeOn() : SimParameters
isSendSpanningTreeUnset() : SimParameters
isSorted : SortedArray< Elem >
IsTimeToClearAccumulator() : ALambdaManager, ALambdaControl
IsTimeToPrint() : ALambdaManager, ALambdaControl
IsTimeToPrint_dU_dLambda() : ALambdaManager, ALambdaControl
isUsed() : Entry< Elem >
isValid : InputAtom
isWater : CompAtom
isZero : ProxyResultVarsizeMsg
it : colvarmodule, colvarbias_meta::hill
it_restart : colvarmodule
it_restart_from_state_file : colvarmodule
it_width : colvarmodule
item() : ResizeArray< Elem >, RequireReduction, SubmitReduction
iterator : IRSet, maxHeap, minHeap, ResizeArray< Elem >, Array< Elem, Size >
ititl : parm
Ivec() : msm::Ivec

- j -

- k -

k : NonbondedExclValue, four_body_consts, AngleValue, BondValue, Transform, msm::Ivec, GridforceLiteGrid, GridforceFullBaseGrid
K : indexed_table_pair, table_pair_params
K1 : PmeGrid, MoaData
k11 : aniso
k1r : MoaData
K2 : PmeGrid, MoaData
k22 : aniso
k2r : MoaData
K3 : PmeGrid, MoaData
k33 : aniso
k3r : MoaData
k_nopad : GridforceFullBaseGrid
k_ub : AngleValue, angle_params
k_vdwa : ComputeNonbondedUtil
k_vdwb : ComputeNonbondedUtil
ka() : msm::IndexRange
kappa : SimParameters, GBISParamStruct
kb() : msm::IndexRange
keep_hills : colvarbias_meta
kernel : ComputeNonbondedCUDA
key_lookup() : colvarparse
kinetic_energy : colvar
kineticEnergy : Controller
kineticEnergyCentered : Controller
kineticEnergyHalfstep : Controller

- l -

l : cr_sortop
LALT : PDBAtom
lambda : colvarmodule::rotation
lambda_schedule : colvarbias_harmonic
lambda_table : ComputeNonbondedUtil
langevin_param() : Molecule
langevin_useBAOAB : SimParameters
langevinDamping : SimParameters
langevinHydrogen : SimParameters
langevinOn : SimParameters
langevinParam : FullAtom
langevinPiston() : Sequencer
langevinPiston1() : Controller
langevinPiston2() : Controller
langevinPiston_strainRate : Controller
langevinPistonBarrier : SimParameters
langevinPistonDecay : SimParameters
langevinPistonOn : SimParameters
langevinPistonPeriod : SimParameters
langevinPistonTarget : SimParameters
langevinPistonTemp : SimParameters
langevinTemp : SimParameters
langevinVelocities() : Sequencer
langevinVelocitiesBBK1() : Sequencer
langevinVelocitiesBBK2() : Sequencer
lastAtomsForcedBegin : GlobalMaster
lastAtomsForcedEnd : GlobalMaster
lastForcesBegin : GlobalMaster
lastLdbStep : SimParameters
lastResid : ResidueLookupElem
latqueue : CollectionMaster::CollectVectorSequence
Lattice() : Lattice
lattice : SimParameters, Flags, SetLatticeMsg, Patch, OptPmePencil< T >, PmePencil< T >, PmeTransMsg, PmeGridMsg, ComputeNonbondedCUDA, MsmSerialCoordMsg, ComputeMsmMgr, FmmSerialCoordMsg, ExtCoordMsg, colvarproxy_namd, CollectionMaster::CollectVectorInstance
LCHAIN : PDBAtom
LCOOR : PDBAtom
LCOORPREC : PDBAtom
LCPONeighborList() : LCPONeighborList
LCPOOn : SimParameters
lcpoType : Patch, ComputeLCPO
lcpoTypeBox : Patch, ComputeLCPO
lcpoTypeBoxClosed() : Patch
lcpoTypeComputeList : Patch
lcpoTypeList : ProxyDataMsg
ldBalancer : SimParameters
ldBarrierHandle : LdbCoordinator
ldbBackgroundScaling : SimParameters
LdbCoordinator() : LdbCoordinator
ldbCoordinator : Node, BOCgroup
ldbCycleNum : LdbCoordinator
ldbHomeBackgroundScaling : SimParameters
ldbPeriod : SimParameters
ldbPMEBackgroundScaling : SimParameters
ldbRelativeGrainsize : SimParameters
ldbStatsFP : LdbCoordinator
ldbSteps : Sequencer, Controller
ldbStrategy : SimParameters
ldbUnloadOne : SimParameters
ldbUnloadOutputPEs : SimParameters
ldbUnloadPME : SimParameters
ldbUnloadZero : SimParameters
ldObjHandle : HomePatch, Compute
ldObjPtr : SimpleBroadcastObject< T >
left : indexed_table_pair, indexed_nbthole_pair, indexed_vdw_pair, vdw_params, angle_params, bond_params
LELEMENT : PDBAtom
len : msm::Array< T >, StreamMessage, PmeGridMsg
Length : PDBAtom
length : Vector, AtomsCntPerPatchMsg, MoveInputAtomsMsg, IMDheader
length2() : Vector
lesFactor : SimParameters, ComputeNonbondedUtil
lesOn : SimParameters, ComputeNonbondedUtil
lesReduceMass : SimParameters
lesReduceTemp : SimParameters
lesScaling : ComputeNonbondedUtil
level : msm::BlockIndex
LFOOT : PDBAtom
limitDist : SimParameters
line_marker : colvarmodule
linear_interpolate() : GridforceLiteGrid
linenumber : FileStack
LINSERT : PDBAtom
List() : AGroup
listNode() : listNode
LJcorrection : SimParameters
ljEnergy : Controller
ljEnergy_f : Controller
ljEnergy_f_left : Controller
ljEnergy_ti_1 : Controller
ljEnergy_ti_2 : Controller
ljTable : ComputeNonbondedUtil
LJTable() : LJTable
lk_maxgridpts : NL_Msm_t
lk_maxlevels : NL_Msm_t
lk_maxwts : NL_Msm_t
lk_nlevels : NL_Msm_t
lk_padding : NL_Msm_t
lk_srad : NL_Msm_t
LNAME : PDBAtom
load : UniqueSetRaw< Elem >, UniqueSet< Elem >, SortedArray< Elem >, ScriptTcl, InfoRecord
load_atoms() : colvarproxy_namd, colvarproxy, colvarmodule
load_coords() : colvarproxy_namd, colvarproxy, colvarmodule
loadComputeMap : ComputeMap, SimParameters
loadmatrix() : Matrix4
loadTuples() : ComputeHomeTuples< T, S, P >
localActivePatches : ComputeNonbondedCUDA
localComputeRecords : ComputeNonbondedCUDA
localHostedPatches : ComputeNonbondedCUDA
localID() : AtomMap
localIndex : TholeElem, ExclElem, ComputeNonbondedCUDA::patch_record, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
LocalLBInfoMsg() : LocalLBInfoMsg
LOCALMOD() : infostream, datastream
localStart : ComputeNonbondedCUDA::patch_record
localWorkMsg : Compute
localWorkMsg2 : ComputeNonbondedCUDA
LOCC : PDBAtom
LOCCPREC : PDBAtom
lock : PmeSharedUntransMsg, PmeSharedTransMsg
log() : colvarproxy_namd, colvarproxy, colvarmodule
lonepairs : SimParameters
longSplitting : SimParameters
lookat() : Matrix4
lookup() : ResidueLookupElem
lookupCstPool() : HashPool< T >
loop : DataExchanger
low : netint
loweAndersenCutoff : SimParameters
loweAndersenFinish() : HomePatch
loweAndersenOn : SimParameters
loweAndersenRate : SimParameters
loweAndersenTemp : SimParameters
loweAndersenVelocities() : HomePatch
lower() : msm::IndexRange
lower_boundaries : colvar_grid< T >
lower_boundary : colvar
lower_wall : colvar
lower_wall_k : colvar
lowest : netint
LRESNAME : PDBAtom
LRESSEQ : PDBAtom
LSEGNAME : PDBAtom
LSERIAL : PDBAtom
LTEMPF : PDBAtom
LTEMPFPREC : PDBAtom
LTYPE : PDBAtom
lyzd : NL_Msm_t
lyzd_f : NL_Msm_t
lzd : NL_Msm_t
lzd_f : NL_Msm_t

- m -

M : OptPmeRealSpace
m_Kf : ARestraint
m_LambdaKf : ARestraint
m_LambdaRef : ARestraint
m_NumGroups : ARestraint
m_pCOMs : ARestraint
m_pGroups : ARestraint
m_x : AVector
m_y : AVector
m_z : AVector
main : main, colvar::distance_z
maingrid : GridforceFullSubGrid
makeHeaps() : Rebalancer
makePatches() : PatchMap
makeTwoHeaps() : Rebalancer
mallocTest : Node, SimParameters
mallocTest_size : Node
mallocTestQd() : Node
many_allowed : ParseOptions::DataElement
many_to_many_data : OptPmePencil< T >
many_to_many_nb : OptPmePencil< T >
many_to_many_recv_grid() : OptPmeZPencil
many_to_many_recv_trans() : OptPmeXPencil, OptPmeYPencil
many_to_many_recv_untrans() : OptPmeYPencil, OptPmeZPencil
many_to_many_send() : OptPmeYPencil
many_to_many_send_trans() : OptPmeZPencil
many_to_many_send_ungrid() : OptPmeZPencil
many_to_many_send_untrans() : OptPmeXPencil
map : MsmBlockKernel< Vtype, Mtype >, MsmGridCutoffKernel< Vtype, Mtype >, msm::PatchData, ComputeMsmMgr
map_grid() : colvar_grid< T >
mapComputes() : WorkDistrib
mapData() : ComputeMsmMgr
margin : SimParameters
marginViolations : HomePatch, Controller
martiniDielAllow : SimParameters
martiniSwitching : SimParameters
mass : atom_constants, FullAtom, ComputeGBISAtom, colvarmodule::atom
Masses : parm
massIdx : OutputAtomRecord::shortVals, BasicAtomInfo
MASTER : PDBData
master : ComputeNonbondedCUDA, NonbondedCUDASlaveMsg, SlaveInitMsg
masterPe : ComputeNonbondedCUDA
mat : Matrix4Symmetry, Matrix4
match() : colvarmodule::quaternion
MathArray() : MathArray< Elem, Size >
matrix() : colvarmodule::rotation
matrix2d() : colvarmodule::matrix2d< T, outer_length, inner_length >
Matrix4() : Matrix4
Matrix4Symmetry() : Matrix4Symmetry
Matrix4TMD() : Matrix4TMD
MAX : MsmProfiler, MsmTimer
max : msm::Array< T >, ExclusionCheck
max_a() : PatchMap
max_b() : PatchMap
max_c() : PatchMap
max_lyzd : NL_Msm_t
max_lzd : NL_Msm_t
MAX_NSTENCIL_SIZE : ComputeMsmMgr
MAX_NSTENCIL_SKIP_ZERO : ComputeMsmMgr
MAX_POLY_DEGREE : ComputeMsmMgr
maxAtomMovement : Flags
maxatoms : NL_Msm_t
maxbins : NL_Msm_t
maxExclusionFlags : SimParameters
maxForceMerged : Flags
maxForceUsed : Flags
maxGroupRadius : Flags, GBISParamStruct
maxHeap() : maxHeap
maxHydrogenGroupSize : Molecule
maximum_value() : colvar_grid_scalar
maximumMove : Sequencer, SimParameters
maxlevels : NL_Msm_t, MsmC1HermiteBlockProxyMsg, MsmBlockProxyMsg
maxMigrationGroupSize : Molecule
maxNumForces : Results
MaxOneAway : PatchMap
MaxOneOrTwoAway : PatchMap
maxPairPart : SimParameters
maxPart : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeLCPO
maxPatches : SimParameters
maxSelfPart : SimParameters
MaxTwoAway : PatchMap
Mbona : parm
measure() : ScriptTcl
measureMemory() : Node
melem : C1Matrix
memusage : memusageinit
memusageinit() : memusageinit
mergeCrossterms : SimParameters
messageBOCCheckIn() : Node
messageEnqueueWork() : WorkDistrib
messageFinishWork() : ComputeNonbondedCUDA
messageRun() : Node
messageStartUp() : Node
mgr : msm::PatchData
mgridforcelist : SimParameters
mgridforceOn : SimParameters
MGridforceParams() : MGridforceParams
MGridforceParamsList() : MGridforceParamsList
mgrLocal : MsmBlockKernel< Vtype, Mtype >, MsmGridCutoffKernel< Vtype, Mtype >
mgrProxy : MsmBlockKernel< Vtype, Mtype >
Migrate() : LdbCoordinator
MigrateAtomsCombinedMsg() : MigrateAtomsCombinedMsg
migrateAtomsMGrp() : ParallelIOMgr
MigrateAtomsMsg() : MigrateAtomsMsg
migrateMsgs : LdbCoordinator
migrationGroupSize : FullAtom
migrationList : MigrateAtomsCombinedMsg, MigrateAtomsMsg
min : ExclusionCheck
min_a() : PatchMap
min_b() : PatchMap
min_c() : PatchMap
min_energy : Controller
min_f_dot_f : Controller
min_f_dot_v : Controller
min_huge_count : Controller
min_v_dot_v : Controller
minAtomsPerPatch : SimParameters
minBabyStep : SimParameters
minHeap() : minHeap
minimizationQuenchVelocity() : Sequencer
minimize() : Sequencer, Controller
minimizeCGOn : SimParameters
minimizeCoefficient : ControllerBroadcasts
minimizeMoveDownhill() : Sequencer
minimizeOn : SimParameters
minimum_value() : colvar_grid_scalar
minLineGoal : SimParameters
minPart : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeLCPO
minpoint() : minpoint
minTinyStep : SimParameters
minVerbose : SimParameters
miscForcesOn : SimParameters
MIStream() : MIStream
mList : MigrationInfo
mod2() : floatcomplex
MODEL : PDBData
modExclCnt : ExclusionSignature
modExclOffset : ExclSigInfo
modified : Exclusion, ExclElem
modifyAppliedForces() : GlobalMaster
modifyForcedAtoms() : GlobalMaster
modifyGroupForces() : GlobalMaster
modifyRequestedAtoms() : GlobalMaster
modifyRequestedGroups() : GlobalMaster
modOffset : ExclusionSignature
mol : ComputeNonbondedUtil
molecule : Node
Molecule() : Molecule
MolInst() : MolInst
mollyAverage() : HomePatch
mollyIter : SimParameters
mollyMollify() : HomePatch
mollyOn : SimParameters
mollyTol : SimParameters
momentumCorrection : ControllerBroadcasts
MOStream() : MOStream
movDragFile : SimParameters
movDragGlobVel : SimParameters
movDragOn : SimParameters
movDragVelFile : SimParameters
moveAllBy() : PatchMgr
moveAtom() : PatchMgr
MovePatch() : MovePatch
movePatch() : PatchMgr
MovePatchesMsg() : MovePatchesMsg
moves : LocalLBInfoMsg
moveto : parm, MoveAtomMsg
moveToNode : ComputeMap::ComputeData
movingConstraintsOn : SimParameters
movingConsVel : SimParameters
Mphia : parm
MPID : InputAtom, HydrogenGroupID, OutputAtomRecord::integerVals
msg : CkCallbackWrapper, PmeSharedUntransMsg, PmeSharedTransMsg, TaggedMsg
msgbuf : HomePatch
msgSize : TaggedMsg
msm::PatchData : ComputeMsmMgr
MSMApprox : SimParameters
MsmBlock : MsmBlock, ComputeMsmMgr
msmBlock : ComputeMsmMgr
msmBlockElementProxy : MsmC1HermiteGridCutoff, MsmGridCutoff
msmBlockElementProxyData : MsmC1HermiteGridCutoffSetupMsg, MsmGridCutoffSetupMsg
MsmBlockKernel() : MsmBlockKernel< Vtype, Mtype >
MsmBlockMap : MsmBlockMap, ComputeMsmMgr
msmBlockProxyData : MsmC1HermiteBlockProxyMsg, MsmBlockProxyMsg
MSMBlockSizeX : SimParameters
MSMBlockSizeY : SimParameters
MSMBlockSizeZ : SimParameters
msmC1HermiteBlock : ComputeMsmMgr
MsmC1HermiteBlock() : MsmC1HermiteBlock
msmC1HermiteGridCutoff : ComputeMsmMgr
MsmC1HermiteGridCutoff() : MsmC1HermiteGridCutoff
msmCompute : ComputeMsmMgr
msmflags : NL_Msm_t
msmGridCutoff : ComputeMsmMgr
MsmGridCutoff() : MsmGridCutoff
msmGridCutoffBroadcast : MsmC1HermiteBlock, MsmBlock
MsmGridCutoffInitMsg() : MsmGridCutoffInitMsg
MsmGridCutoffKernel() : MsmGridCutoffKernel< Vtype, Mtype >
MsmGridCutoffMap : MsmGridCutoffMap, ComputeMsmMgr
msmGridCutoffProxyData : MsmC1HermiteGridCutoffProxyMsg, MsmGridCutoffProxyMsg
msmGridCutoffReduction : MsmC1HermiteBlock, MsmBlock
MSMGridSpacing : SimParameters
MSMLevels : SimParameters
MSMOn : SimParameters
MSMPadding : SimParameters
MsmProfiler() : MsmProfiler
msmProxy : ComputeMsmMgr
MSMQuality : SimParameters
MsmSerialOn : SimParameters
MSMSplit : SimParameters
MsmTimer() : MsmTimer
Mtheta : parm
MTRIX : PDBData
MTSAlgorithm : SimParameters
mult : colvar_grid< T >
multicastMgr : BOCgroup
multiple_replicas : colvarbias_meta
multiplicity : colvar_grid< T >, ImproperValue, DihedralValue, improper_params, dihedral_params
multiply_constant() : colvar_grid< T >
multirefine() : Rebalancer
multmatrix() : Matrix4Symmetry, Matrix4, Matrix4TMD
multnorm3d() : Matrix4
multpoint() : Matrix4Symmetry, Matrix4TMD
multpoint3d() : Matrix4
multpoint4d() : Matrix4
myGrid : OptPmeRealSpace
mygridnum : GridforceGrid
myHandle : LdbCoordinator
myid() : Node
myKSpace : OptPmeXPencil, PmeXPencil
myOMid : LdbCoordinator
myRemove() : IRSet
mySegid : ResidueLookupElem

- n -

n : four_body_consts, msm::BlockIndex
N : SimParameters, OptPmeRealSpace
n_abf_biases : colvarmodule
n_components() : colvar
n_harm_biases : colvarmodule
n_histo_biases : colvarmodule
n_meta_biases : colvarmodule
n_moves : LocalLBInfoMsg
n_sum : GridforceFullBaseGrid
Namd : NamdState
NamdCentLB() : NamdCentLB
NamdDummyLB() : NamdDummyLB
NamdHybridLB() : NamdHybridLB
NamdNborLB() : NamdNborLB
NamdState() : NamdState
name : PDBAtom, ParseOptions::DataElement, ConfigList::ConfigListNode, colvar::cvc, colvarbias, colvar
Nat3 : parm
Natcap : parm
Natom : parm
Natyp : parm
nbinslots : NL_Msm_t
nblock : msm::BlockSend
nblock_wrap : msm::BlockSend
Nbona : parm
nbond : Results
nbondFreq : Controller
Nbonh : parm
nbrhd : NL_Msm_t
nbrhdlen : NL_Msm_t
nbrhdmax : NL_Msm_t
nbthole_array : Parameters
nbthole_pair_tree : Parameters
nbx : NL_Msm_t
nby : NL_Msm_t
nbytes : GridMsg
nbz : NL_Msm_t
nChild : Patch
nComputes : ComputeMapMsg
nComputesExpected : LdbCoordinator
nComputesReported : LdbCoordinator
nd : colvar_grid< T >
ndsplitting() : ComputeMsmMgr
nearest() : Lattice
needs_reply : PmePencil< T >
net_dE : Controller
net_dEdl_elec_1 : Controller
net_dEdl_elec_2 : Controller
net_dEdl_lj_1 : Controller
net_dEdl_lj_2 : Controller
new_count() : colvar_grid_count
new_data : colvar_grid< T >
new_grid() : GridforceGrid
new_hill_freq : colvarbias_meta
new_hills_begin : colvarbias_meta
new_hills_off_grid_begin : colvarbias_meta
new_index() : colvar_grid< T >
newaid : ComputeGlobalResultsMsg
newCid() : PatchMap
newgdef : ComputeGlobalResultsMsg
newInputStream() : Communicate
newlist() : Pairlists, LCPONeighborList
newMinimizeDirection() : Sequencer
newMinimizePosition() : Sequencer
newNode() : ComputeMap
newNodes : ComputeMapChangeMsg
newNumPartitions : ComputeMap, ComputeMapChangeMsg, ComputeMap::ComputeData
newOutputStream() : Communicate
newPid() : ComputeMap
newRefine() : RefineTorusLB
newsize() : Pairlists, LCPONeighborList
next : EntryGlob< Elem >, Entry< Elem >, IRSet, maxHeap, minHeap, Iterator, listNode, ReductionSetData, PAL, nbthole_pair_params, table_pair_params, vdw_pair_params, crossterm_params, improper_params, dihedral_params, StreamMessage, NL_Msm_t, ResidueLookupElem, MGridforceParams, LdbMigrateMsg, heapIterator, ConfigList::ConfigListNode, StringList, FileStack
nextent : msm::IndexRange
nextent_i : GridMsg
nextent_j : GridMsg
nextent_k : GridMsg
nextlist() : Pairlists, LCPONeighborList
nextSequenceNumber : ReductionSet
Nhparm : parm
nhx : ComputeMsmMgr
nhy : ComputeMsmMgr
nhz : ComputeMsmMgr
ni() : msm::IndexRange
nj() : msm::IndexRange
nk() : msm::IndexRange
nlevels : NL_Msm_t, ComputeMsmMgr, MsmC1HermiteBlockProxyMsg, MsmBlockProxyMsg
nLocalComputes : LdbCoordinator
nLocalPatches : LdbCoordinator
nlower : msm::IndexRange
nlower_i : GridMsg
nlower_j : GridMsg
nlower_k : GridMsg
Nmxrs : parm
nn() : msm::IndexRange
Nnb : parm
no_footnote : PDBAtom
node : PatchMap, ComputeMap, nodesort, ProxySpanningTreeMsg, ProxyResultVarsizeMsg, ProxyResultMsg, UnregisterProxyMsg, RegisterProxyMsg, ComputeMap::ComputeData, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, BOCgroup
Node : Node, NamdState
node_process_grid() : PmeZPencil
node_process_trans() : PmeXPencil, PmeYPencil
node_process_untrans() : PmeYPencil, PmeZPencil
nodecount : ProxyMgr
nodeDone() : LdbCoordinator
nodeID : MovePatch, proxyTreeNode
nodePmeMgr : BOCgroup
NodePmeMgr : NodePmeMgr, ComputePmeMgr
NodeProxyMgr() : NodeProxyMgr
nodes : ProxyCombinedResultMsg, ProxyCombinedResultRawMsg
nodeSize : ProxyCombinedResultRawMsg
nodesort() : nodesort
noforce : colvarmodule::atom_group
noGradient : minpoint
nonbondedFrequency : SimParameters
nonbondedGroupSize : CompAtom
nonbondedScaling : SimParameters
NONIC : ComputeMsmMgr
NONIC4 : ComputeMsmMgr
noPatchesOnOne : SimParameters
noPatchesOnOutputPEs : SimParameters
noPatchesOnZero : SimParameters
norm() : colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
norm2() : colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
normal : Results, AngleValue, angle_params
NOT_PROCESSED : CollectionMaster
notfree() : CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
noWork() : ComputePme, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA, ComputeLCPO, Compute
Nparm : parm
npatches : nodesort
nPatches : LdbCoordinator
nPatchesExpected : LdbCoordinator
nPatchesReported : LdbCoordinator
npe : NodePmeInfo
Nphb : parm
Nphia : parm
Nphih : parm
Nptra : parm
nradius : NL_Msm_t
nrange : msm::BlockDiagram, msm::PatchDiagram, msm::PatchSend, msm::BlockSend
nrange_unwrap : msm::PatchSend
nrange_wrap : msm::BlockSend
nrangeCutoff : msm::BlockDiagram
nrangeProlongated : msm::BlockDiagram
nrangeRestricted : msm::BlockDiagram
nRegisteredObjs : LdbCoordinator
Nres : parm
Nspm : parm
Nspsol : parm
nStatsMessagesExpected : LdbCoordinator
nStatsMessagesReceived : LdbCoordinator
Nstencil : ComputeMsmMgr
nt : colvar_grid< T >
Ntheta : parm
Ntheth : parm
Nttyp : parm
Ntype2d : parm
Ntypes : parm
nu : InterpParams_t
num() : ParseOptions
NUM_APPROX : ComputeMsmMgr
NUM_APPROX_FORMS : ComputeMsmMgr
num_atom_records : ComputeNonbondedCUDA
num_atoms() : PDB
num_clients : MoaData
num_clients_bh : MoaData
num_clients_qh : MoaData
num_clients_sh : MoaData
num_deg_freedom() : Molecule
num_fixed_atoms() : Molecule
num_fixed_groups() : Molecule
num_force_records : ComputeNonbondedCUDA
num_group_deg_freedom() : Molecule
num_local_atom_records : ComputeNonbondedCUDA
num_remote_atom_records : ComputeNonbondedCUDA
NUM_SPLIT : ComputeMsmMgr
numAcceptors : Molecule
numAcksOutstanding : ParallelIOMgr
Numang : parm
NumAngleParams : Parameters
numAngles : MolInfoMsg, Molecule
numAnisos : Molecule
numAtoms : Patch, Molecule, MigrateAtomsCombinedMsg, patchInfo, ComputePatchPair, ComputePatch, nonbonded, ComputeNonbondedCUDA::patch_record, MsmSerialCoordMsg, ComputeLCPO, ComputeHomePatch, GBISCoordMsg, FmmSerialCoordMsg, ExtCoordMsg
numatoms : NL_Msm_t
numAtomsPair : SimParameters
numAtomsPair2 : SimParameters
numAtomsSelf : SimParameters
numAtomsSelf2 : SimParameters
numAvailable() : Rebalancer
numaway_a() : PatchMap
numaway_b() : PatchMap
numaway_c() : PatchMap
number_of_colvars() : colvar_grid< T >
number_of_points() : colvar_grid< T >
numbins : NL_Msm_t
Numbnd : parm
NumBondParams : Parameters
numBonds : MolInfoMsg, Molecule
numCalcAngles : MolInfoMsg, Molecule
numCalcAnisos : Molecule
numCalcBonds : MolInfoMsg, Molecule
numCalcCrossterms : MolInfoMsg, Molecule
numCalcDihedrals : MolInfoMsg, Molecule
numCalcExclusions : MolInfoMsg, Molecule
numCalcImpropers : MolInfoMsg, Molecule
numCalcTholes : Molecule
numChildren : DataExchanger
numCids() : PatchMap
numComputes : ComputeMap, Rebalancer, LdbCoordinator
numConsForce : Molecule
numConsTorque : Molecule
numConstraints : Molecule
NumCosAngles : Parameters
NumCrosstermParams : Parameters
numCrossterms : MolInfoMsg, Molecule
numDegFreedom : Controller
NumDihedralParams : Parameters
numDihedrals : MolInfoMsg, Molecule
numDonors : Molecule
numDrudeAtoms : Molecule
numElements() : IRSet, maxHeap, minHeap
numenerentries : Parameters
numExclusions : MolInfoMsg, Molecule
numExPressureAtoms : Molecule
numFepFinal : Molecule
numFepInitial : Molecule
numFixedAtoms : Patch, Molecule
numFixedGroups : HydroBasedMsg, Molecule
numFixedRigidBonds : HydroBasedMsg, Molecule
numFreeAtoms : ComputeNonbondedCUDA::patch_record
numGaussPair : Molecule
numGBISPairlists : ComputeNonbondedSelf, ComputeNonbondedPair
numGoAtoms : Molecule
NumGoChains : Molecule
numGridCutoff : ComputeMsmMgr
numGridforceGrids : Molecule
numGridforces : Molecule
numHomePatches() : PatchMap
numHydrogenGroups : Molecule
NumImproperParams : Parameters
numImpropers : MolInfoMsg, Molecule
numinputprocs : SimParameters
numLevels() : ComputeMsmMgr
numLJPair : Molecule
numLonepairs : Molecule
numLphosts : Molecule
numMigrationGroups : Molecule
numMlBuf : HomePatch
numMovDrag : Molecule
numMultipleDihedrals : Molecule
numMultipleImpropers : Molecule
NumNbtholePairParams : Parameters
numNewNodes : ComputeMapChangeMsg
numNewNumPartitions : ComputeMapChangeMsg
numNodes() : Node
numNodesWithPatches() : PatchMap
numNodesWithProxies : ProxyNodeAwareSpanningTreeMsg
numOffset : TupleSignature
numoutputprocs : SimParameters
numoutputwrts : SimParameters
numPair : Molecule
numParticles : ComputeDPMEResultsMsg, ComputeDPMEDataMsg
numPartitions : ComputeMap, ComputeMap::ComputeData
numParts : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeLCPO
numPatches : PatchMap, Rebalancer, PatchProxyListMsg, GBISParamStruct
numPatchesOnNode() : PatchMap
numPes : proxyTreeNode
numPesAvailable : Rebalancer
numPesOfNode : ProxyNodeAwareSpanningTreeMsg
numPids : ComputeMap, ComputeMap::ComputeData
numPidsAllocated : ComputeMap
numProxies : ProxyMgr, Rebalancer, ProxyListInfo
numRealBonds : Molecule
numRecvs : msm::PatchDiagram
numRecvsCharge : msm::BlockDiagram
numRecvsPotential : msm::BlockDiagram
numrep : msm::FoldFactor
numRigidBonds : MolInfoMsg, Molecule
numRotDrag : Molecule
numSlaves : ComputeNonbondedCUDA
numStepsToRun : LdbCoordinator
numStirredAtoms : Molecule
numSubgrids : GridforceFullBaseGrid
NumTablePairParams : Parameters
NumTableParams : Parameters
numTholes : Molecule
numTotalExclusions : Molecule
numTraceSteps : SimParameters
NumVdwPairParams : Parameters
NumVdwParams : Parameters
NumVdwParamsAssigned : Parameters
numVirialContrib : ComputeMsmMgr
nx : NL_Msm_t, OptPmeFFTMsg, LocalPmeInfo, PmeTransMsg, Int3, Int2, colvar_grid< T >
nxc : colvar_grid< T >
ny : NL_Msm_t, OptPmeXPencil, PmeXPencil, PmeUntransMsg, Int3, Int2
ny_after_transpose : LocalPmeInfo
nz : NL_Msm_t, OptPmeXPencil, PmeXPencil, Int3

- o -

obj : Entry< Elem >
Object() : Sync, ReductionMgr, ProxyMgr, PatchMgr, PatchMap, Node, LdbCoordinator, ComputeMap, CollectionMgr, CollectionMaster, BroadcastMgr, AtomMap
ObjectArena() : ObjectArena< Type >
ObjectOnPe() : PatchMap
OBSLTE : PDBData
occupancy() : PDBAtom
off_diagonal : Tensor
offset : Lattice, TupleSignature, MoveAllByMsg, GridforceFullBaseGrid, nonbonded, ComputeNonbondedCUDA::compute_record
offset_a() : Lattice
offset_b() : Lattice
offset_c() : Lattice
okay() : ConfigList
old_pos : colvarmodule::atom_group
oldProcessor : computeInfo
omega : InterpParams_t, ComputeMsmMgr
oneAwayNeighbors() : PatchMap
oneOrTwoAwayNeighbors() : PatchMap
open() : OwnerBox< Owner, Data >, Box< Owner, Data >
openSync() : Sync
OperationStatus : CollectionMaster
operator * : Vector, UniqueSetIter< T >, Tensor, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, C1Matrix, C1Vector, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rmatrix, colvarmodule::vector1d< T, length >, colvarmodule::rvector
operator *=() : Vector, Tensor, MathArray< Elem, Size >, AVector, floatcomplex, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
operator const Real &() : HashReal
operator const T &() : HashPoolAdaptorT< T >
operator cvm::quaternion() : colvarvalue
operator cvm::real() : colvarvalue
operator cvm::rvector() : colvarvalue
operator Real &() : HashReal
operator T &() : HashPoolAdaptorT< T >
operator T *() : colvarmodule::vector1d< T, length >
operator T **() : colvarmodule::matrix2d< T, outer_length, inner_length >
operator!= : Vector, UniqueSetIter< T >, Tensor, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, colvarmodule::rvector
operator()() : WorkDistrib::pe_sortop_compact, WorkDistrib::pe_sortop_diffuse, patch_sortop_curve_c, patch_sortop_curve_b, patch_sortop_curve_a, pe_sortop_coord_y, pe_sortop_coord_x, pe_sortop_bit_reversed, sortop_z, sortop_y, sortop_x, msm::Grid< T >, msm::GridFixed< T, N >, atomID_less, ijpair_sortop_bit_reversed, sortop_bit_reversed, cr_sortop, exlist_sortop
operator+ : Vector, Tensor, C1Vector, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rvector
operator++() : UniqueSetIter< T >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >
operator+=() : Vector, Tensor, msm::Grid< T >, msm::GridFixed< T, N >, C1Vector, MathArray< Elem, Size >, AVector, floatcomplex, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
operator- : Vector, Tensor, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rvector
operator-=() : Vector, Tensor, MathArray< Elem, Size >, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
operator->() : UniqueSetIter< T >, ResizeArrayIter< T >
operator/ : Vector, Tensor, MathArray< Elem, Size >, AVector, colvarmodule::quaternion, colvarmodule::rvector
operator/=() : Vector, Tensor, MathArray< Elem, Size >, AVector, colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
operator< : nodesort, Exclusion, MovePatch, InputAtom, HydrogenGroupID, HomePatchElem, vmdforce, TholeElem, ExclElem, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem, colvarbias_meta::hill
operator<< : infostream, datastream, colvarmodule::quaternion, colvarmodule::matrix2d< T, outer_length, inner_length >, colvarmodule::vector1d< T, length >, colvarbias_meta::hill
operator<= : msm::IndexRange, WorkIndex, colvarbias_meta::hill
operator=() : Vector, UniqueSortedArray< Elem >, UniqueSetRaw< Elem >, Entry< Elem >, UniqueSetIter< T >, UniqueSet< Elem >, Tensor, ExclusionSignature, AtomSignature, TupleSignature, SortedArray< Elem >, SortableResizeArray< Elem >, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, Flags, proxyTreeNode, msm::Array< T >, ExclusionCheck, Matrix4, MathArray< Elem, Size >, HomePatchElem, vmdforce, AVector, ALambdaControl, AGroup, floatcomplex, colvarvalue, colvarmodule::matrix2d< T, outer_length, inner_length >, colvarmodule::vector1d< T, length >, colvarmodule::rvector, Array< Elem, Size >
operator==() : nodesort, Vector, UniqueSetIter< T >, Tensor, ExclusionSignature, AtomSignature, TupleSignature, Exclusion, ResizeArrayPrimIter< T >, ResizeArrayIter< T >, ProxyElem, MovePatch, ClusterCoorElem, ClusterElem, msm::Ivec, HomePatchElem, vmdforce, TholeElem, ExclElem, ImproperElem, TuplePatchElem, PatchElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem, colvarmodule::rvector, colvarbias_meta::hill, BOID, TaggedMsg, BroadcastClientElem
operator> : colvarbias_meta::hill
operator>= : colvarbias_meta::hill
operator>> : colvarmodule::quaternion, colvarparse::read_block
operator[]() : Vector, ResizeArray< Elem >, msm::Array< T >, AVector, ARestraintManager, ALambdaManager, AGroup, HashPool< T >, colvarmodule::quaternion, colvarmodule::rvector, Array< Elem, Size >
optional() : ParseOptions
optionalB() : ParseOptions
OptPmeCompute : OptPmeCompute, OptPmeMgr
OptPmeMgr() : OptPmeMgr
OptPmePencil() : OptPmePencil< T >
OptPmePencilInitMsg() : OptPmePencilInitMsg
OptPmePencilMapX() : OptPmePencilMapX
OptPmePencilMapY() : OptPmePencilMapY
OptPmePencilMapZ() : OptPmePencilMapZ
OptPmeRealSpace() : OptPmeRealSpace
OptPmeXPencil() : OptPmeXPencil
OptPmeYPencil() : OptPmeYPencil
OptPmeZPencil() : OptPmeZPencil
order : PmeGrid, MoaData
order_init() : OptPmePencil< T >, PmePencil< T >
orientation() : colvar::orientation
orientation_angle() : colvar::orientation_angle
orig_x : MoaData
orig_y : MoaData
orig_z : MoaData
origin : PatchMap, Lattice, GridforceLiteGrid, GridforceFullBaseGrid
originalPosition : GlobalMasterMisc
origMaxLoad : Rebalancer
origPe : ProxyGBISP3DataMsg, ProxyGBISP2ResultMsg, ProxyGBISP2DataMsg, ProxyGBISP1ResultMsg
ORIGX : PDBData
ortho() : Matrix4
ortho2() : Matrix4
orthogonal() : Lattice
Out() : AVector
outer() : Tensor, colvarmodule::rvector
outerAdd() : Tensor
Output() : Output, AVector
output : TupleSignature, Node
output_prefix : colvarproxy_namd, colvarproxy, colvarmodule
output_prefix_str : colvarproxy_namd
output_traj() : colvarbias_meta::hill
output_width() : colvarvalue, colvarmodule::quaternion, colvarmodule::rvector
outputCudaTiming : SimParameters
outputEnergies : SimParameters
outputExtendedSystem() : Controller
outputFepEnergy() : Controller
outputFilename : SimParameters
outputMaps : SimParameters
outputMomenta : SimParameters
outputPairlists : SimParameters
outputPatchComputeMaps() : Node
outputPatchDetails : SimParameters
outputPressure : SimParameters
outputTiEnergy() : Controller
outputTiming : SimParameters
overLoad : Rebalancer
OwnerBox() : OwnerBox< Owner, Data >
OwnerBox<Owner,Data> : Box< Owner, Data >

- p -

P : Rebalancer
p : Rebalancer::pcpair, Patch, TholeElem, ComputePatchPair, ComputePatch, nonbonded, ExclElem, ComputeNonbondedCUDA::patch_record, ImproperElem, TuplePatchElem, PatchElem, ComputeGlobalDataMsg, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
p2leg_opt() : colvarvalue
p_0_sortValues : ComputeNonbondedWorkArrays
p_avg : Patch
p_sum : GridforceFullBaseGrid
pack() : ExclusionSignature, AtomSignature, TupleSignature, ProxySpanningTreeMsg, ProxyResultMsg, MovePatchesMsg, PatchMap, MigrateAtomsCombinedMsg, MigrateAtomsMsg, GridforceLiteGrid, GridforceFullSubGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid, ComputeMap, ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, ComputeConsForceMsg, DataStreamMsg
pack_data() : MGridforceParamsList
pack_grid() : GridforceGrid
packSize() : PatchMap
pad : AlignVector
pad_n : GridforceFullBaseGrid
pad_p : GridforceFullBaseGrid
padding : ProxyResultVarsizeMsg, ComputeMsmMgr
pairC12 : Molecule
pairC6 : Molecule
pairElectForceIndex : ComputeNonbondedUtil
pairInteractionGroup1 : SimParameters
pairInteractionGroup2 : SimParameters
pairInteractionOn : SimParameters, ComputeNonbondedUtil
pairInteractionSelf : SimParameters, ComputeNonbondedUtil
pairlist : ComputeNonbondedWorkArrays
pairlist2 : ComputeNonbondedWorkArrays
pairlistDist : SimParameters
pairlistGrow : SimParameters
pairlisti : ComputeNonbondedWorkArrays
pairlistm : ComputeNonbondedWorkArrays
pairlistmA1 : ComputeNonbondedWorkArrays
pairlistmA2 : ComputeNonbondedWorkArrays
pairlistMinProcs : SimParameters
pairlistnA0 : ComputeNonbondedWorkArrays
pairlistnA1 : ComputeNonbondedWorkArrays
pairlistnA2 : ComputeNonbondedWorkArrays
pairlistnAlch : ComputeNonbondedWorkArrays
pairlists : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair
Pairlists() : Pairlists
pairlistsAge : Sequencer
pairlistsAreValid : Sequencer
pairlistShrink : SimParameters
pairlistsPerCycle : SimParameters
pairlistsValid : ComputeNonbondedSelf, ComputeNonbondedPair
pairlistTolerance : Flags, ComputeNonbondedSelf, ComputeNonbondedPair
pairlistTrigger : SimParameters
pairlistWarningIndex : ComputeNonbondedUtil
pairlistWarnings : Controller
pairlistx : ComputeNonbondedWorkArrays
pairlistxA1 : ComputeNonbondedWorkArrays
pairlistxA2 : ComputeNonbondedWorkArrays
pairVDWForceIndex : ComputeNonbondedUtil
papiMeasureBarrier() : Node
ParallelIOMgr() : ParallelIOMgr
param : ScriptParamMsg
parameters : Node
Parameters() : Parameters
params : ComputeNonbondedSelf, ComputeNonbondedPair
paraTypeCharmmOn : SimParameters
paraTypeXplorOn : SimParameters
parent : ParseOptions::DataElement, GridforceFullSubGrid, DataExchanger
parent_ptr : ParseOptions::DataElement
parm() : parm
parse : PDBAtom, colvarmodule::atom_group, colvarmodule
parse_analysis() : colvar
parse_group() : colvar::cvc
Parse_Mode : colvarparse
parse_normal : colvarparse
parse_params() : colvar_grid< T >
parse_silent : colvarparse
ParseOptions() : ParseOptions
particles : ComputeDPMEDataMsg
partition : RecBisection, ComputeMap, CompAtom, ComputeMap::ComputeData
partner : AtomCstInfo, atom_constants
patch : PatchMap, Sequencer, ProxyUsageKey, ProxySpanningTreeMsg, ProxyCombinedResultMsg, ProxyCombinedResultRawMsg, ProxyNodeAwareSpanningTreeMsg, ProxyResultVarsizeMsg, ProxyResultMsg, ProxyDataMsg, UnregisterProxyMsg, RegisterProxyMsg, ProxyGBISP3DataMsg, ProxyGBISP2ResultMsg, ProxyGBISP2DataMsg, ProxyGBISP1ResultMsg, HomePatchElem, ComputePatchPair, ComputePatch, ComputeLCPO, ComputeHomePatch
Patch() : Patch
patch1 : computeInfo
patch2 : computeInfo
patch_record() : ComputeNonbondedCUDA::patch_record
patch_sortop_curve_a() : patch_sortop_curve_a
patch_sortop_curve_b() : patch_sortop_curve_b
patch_sortop_curve_c() : patch_sortop_curve_c
patchArray : LdbCoordinator
patchCnt : MovePatchAtomsMsg
PatchData() : msm::PatchData
patchDimension : SimParameters
PatchElem() : PatchElem
patches : Rebalancer
patchHandles : LdbCoordinator
patchID : ProxyListInfo, ProxyElem, Patch, PatchGridElem, msm::PatchSend, OptPmeGridMsg, ComputePatchPair, ComputePatch, GBISParamStruct, ComputeNonbondedCUDA::patch_record, msm::PatchData, ComputeLCPO, TuplePatchElem, PatchElem
patchIDs : PatchProxyListMsg
patchList : msm::Map, ComputeHomePatches
patchLoad() : LdbCoordinator
PatchMap : PatchMap, PatchMgr
patchMap : Node, LdbCoordinator, ComputeNonbondedCUDA, ComputeHomeTuples< T, S, P >, ComputeHomePatches
patchMapData : PatchMapMsg
patchMapInit() : WorkDistrib
PatchMgr : PatchMgr, HomePatch
patchMgr : BOCgroup
patchNAtoms : LdbCoordinator
PatchProxyListMsg() : PatchProxyListMsg
patchPtr : ComputeMsmMgr
patchPtrArray() : ComputeMsmMgr
PatchReady() : Sync
patchReady() : Compute
PatchRec() : ComputeMap::PatchRec
patchRecords : ComputeNonbondedCUDA
patchSet : processorInfo
pauseWork() : LdbCoordinator
pcgrid : Rebalancer
pcpair() : Rebalancer::pcpair
pd : msm::PatchData
pdb : Node
PDB() : PDB
PDBAtom() : PDBAtom
PDBAtomRecord() : PDBAtomRecord
PDBData() : PDBData
PDBFormatStyle : PDBData
PDBHetatm() : PDBHetatm
PDBNames : PDBData
PDBPossibleAtoms : PDBAtom
PDBType : PDBData
PDBUnknown() : PDBUnknown
PE : StreamMessage
pe_sortop_bit_reversed() : pe_sortop_bit_reversed
pe_sortop_coord_x() : pe_sortop_coord_x
pe_sortop_coord_y() : pe_sortop_coord_y
pe_start : NodePmeInfo
peCompactOrdering : WorkDistrib
peCompactOrderingIndex : WorkDistrib
peDiffuseOrdering : WorkDistrib
peDiffuseOrderingIndex : WorkDistrib
peIDs : proxyTreeNode
period : colvar::cvc, colvar
periodic : colvar_grid< T >
periodic_a() : PatchMap
periodic_b() : PatchMap
periodic_boundaries() : colvar
periodic_c() : PatchMap
pes : Rebalancer
pExt : Patch, ComputePatchPair, ComputePatch, nonbonded
pgc : MsmGridCutoffKernel< Vtype, Mtype >
pgvc : MsmGridCutoffKernel< Vtype, Mtype >
Phase : parm
PhiStencil : ComputeMsmMgr
pi_ewaldcof : ComputeNonbondedUtil
pid : PatchMap, ComputeMap, MovePatch, MovePatchesMsg, LocalID, HomePatchElem, ComputeNonbondedCUDA::compute_record, ComputeMap::PatchRec
pidList : MovePatchAtomsMsg, AtomsCntPerPatchMsg
pids : ComputeMap::ComputeData
Pk : parm
plcutoff : nonbonded
plExtLen : ProxyDataMsg
plLen : ProxyDataMsg
PluginIOMgr() : PluginIOMgr
pmap : patch_sortop_curve_c, patch_sortop_curve_b, patch_sortop_curve_a
pmax : GridforceFullSubGrid
pme_kspace() : OptPmeXPencil, PmeXPencil
PMEBarrier : SimParameters
PMEEwaldCoefficient : SimParameters
PMEGridSizeX : SimParameters
PMEGridSizeY : SimParameters
PMEGridSizeZ : SimParameters
PMEGridSpacing : SimParameters
PMEInterpOrder : SimParameters
PmeKSpace() : PmeKSpace
PMEMinPoints : SimParameters
PMEMinSlices : SimParameters
pmeNodeProxy : PmePencilInitMsgData
PMEOn : SimParameters
PmePencil() : PmePencil< T >
PmePencilInitMsg() : PmePencilInitMsg
PmePencilMap() : PmePencilMap
PMEPencils : SimParameters
PMEPencilsX : SimParameters
PMEPencilsXLayout : SimParameters
PMEPencilsY : SimParameters
PMEPencilsYLayout : SimParameters
PMEPencilsZ : SimParameters
PMEProcessors : SimParameters
pmeProxy : OptPmePencilInitMsgData, PmePencilInitMsgData
PmeRealSpace() : PmeRealSpace
PMESendOrder : SimParameters
PMETolerance : SimParameters
PmeXPencil() : PmeXPencil
PmeYPencil() : PmeYPencil
PmeZPencil() : PmeZPencil
pmin : GridforceFullSubGrid
Pn : parm
Pointer() : Pointer
pointerToGaussBeg : Molecule
pointerToGaussEnd : Molecule
pointerToGoBeg : Molecule
pointerToGoEnd : Molecule
pointerToLJBeg : Molecule
pointerToLJEnd : Molecule
PolyDegree : ComputeMsmMgr
popn : parm
populateInitial() : PmePencilMap
pos : ComputeLCPO, colvarmodule::atom
pos1 : colvarmodule::rotation
pos2 : colvarmodule::rotation
posExt : ComputeLCPO
position : CompAtom, msm::AtomCoord, ComputeMsmSerialAtom, ComputeGBISAtom, ComputeFmmSerialAtom, ComputeExtAtom
position_derivative_inner() : colvarmodule::quaternion
position_dist2() : colvarproxy_namd, colvarproxy, colvarmodule
position_distance() : colvarproxy_namd, colvarproxy, colvarmodule
positionBox : Patch, ComputePatchPair, ComputePatch, ComputeNonbondedCUDA::patch_record, ComputeLCPO, TuplePatchElem, PatchElem
positionBoxClosed() : Patch
positionComputeList : Patch
positionExtList : ProxyDataMsg
positionList : ProxyDataMsg
positionRescaleFactor : Controller, ControllerBroadcasts
positions : colvarmodule::atom_group, colvarproxy_namd
positions_shifted() : colvarmodule::atom_group
positionsReady() : Patch, HomePatch
poten_fp : GridforceFullBaseGrid
potential_energy : colvar
ppbonded : Controller
ppint : Controller
ppnonbonded : Controller
preadln() : parm
precisions : CollectionMgr::CollectVectorInstance
preCreateHomePatch() : PatchMgr
pressure : Controller
pressure_avg : Controller
pressure_nbond : Controller
pressure_normal : Controller
pressure_slow : Controller
pressure_tavg : Controller
pressureProfileAtomTypes : SimParameters, TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
pressureProfileAverage : Controller
pressureProfileCount : Controller
pressureProfileData : ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
pressureProfileEwaldOn : SimParameters
pressureProfileEwaldX : SimParameters
pressureProfileEwaldY : SimParameters
pressureProfileEwaldZ : SimParameters
pressureProfileFreq : SimParameters
pressureProfileMin : TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
pressureProfileOn : SimParameters, ComputeNonbondedUtil
PressureProfileReduction() : PressureProfileReduction
pressureProfileReduction : Sequencer, nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeHomeTuples< T, S, P >
pressureProfileSlabs : SimParameters, Controller, TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, ComputeHomeTuples< T, S, P >, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
pressureProfileThickness : TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
previous_NAMD_step : colvarproxy_namd
print() : IRSet, MsmProfiler, MsmTimer, MoaData
print_angle_params() : Parameters
print_atoms() : Molecule
print_bond_params() : Parameters
print_bonds() : Molecule
print_crossterm_params() : Parameters
print_dihedral_params() : Parameters
Print_dU_dLambda_Info() : ARestraintManager
Print_dU_dLambda_Summary() : ALambdaManager
print_exclusions() : Molecule
print_go_params() : Molecule
print_go_sigmas() : Molecule
print_improper_params() : Parameters
Print_MCTI_Integration() : ALambdaManager
print_nbthole_pair_params() : Parameters
print_param_summary() : Parameters
print_vdw_pair_params() : Parameters
print_vdw_params() : Parameters
printBadContacts : SimParameters
printComputeMap() : ComputeMap
printDynamicsEnergies() : Controller
printEnergies() : Controller
PrintEnergyInfo() : ARestraintManager
printExclusions : SimParameters
printFepMessage() : Controller
PrintHeader() : ALambdaManager, ALambdaControl
PrintInfo() : ADiheRestraint, AnAngleRestraint, ADistRestraint, APosRestraint, ARestraint
PrintLambdaHeader() : ALambdaManager, ALambdaControl
printLoads() : Rebalancer
printLocalLdbReport() : LdbCoordinator
printMinimizeEnergies() : Controller
printOut() : ProxyNodeAwareSpanningTreeMsg
printPatchMap() : PatchMap
PrintPreInfo() : ARestraintManager
printRequiredProxies() : LdbCoordinator
PrintRestraintInfo() : ARestraintManager
printResults() : Rebalancer
PrintSomeSpaces() : ALambdaManager
printSummary() : Rebalancer
printTiMessage() : Controller
printTiming() : Controller
priority : Compute, MsmGridCutoffKernel< Vtype, Mtype >
PriorityQueue() : msm::PriorityQueue< T >
processData() : GlobalMaster
processor : ProxyUsageKey, patchInfo, computeInfo
processorArray : LdbCoordinator
processorInfo() : processorInfo
processors : Rebalancer
procID : ProxyNodeAwareSpanningTreeMsg
procNum() : OptPmePencilMapZ, OptPmePencilMapY, OptPmePencilMapX, PmePencilMap, MsmGridCutoffMap, MsmBlockMap
procTrans() : ComputePmeMgr
procUntrans() : ComputePmeMgr
project_hills() : colvarbias_meta
projLineVec : nonbonded
PROLONGATE : MsmTimer
prolongation() : MsmC1HermiteBlock, MsmBlock
prolongationKernel() : MsmBlockKernel< Vtype, Mtype >
promote() : colvarmodule::quaternion
proStencil : MsmBlockKernel< Vtype, Mtype >
proxies : processorInfo
proxiesOn : patchInfo
proxy : colvarmodule
ProxyElem() : ProxyElem
proxyList : ProxyListInfo
proxylist : ProxyTree
proxyListLen : PatchProxyListMsg
proxyMgr : BOCgroup
ProxyMgr() : ProxyMgr
proxyMsgCount : ProxyTree
ProxyPatch() : ProxyPatch
proxyPatch : ProxyElem
proxyPEs : PatchProxyListMsg
proxyRecvSpanningTree : SimParameters
proxySendSpanningTree : SimParameters
ProxyTree() : ProxyTree
proxyTreeBranchFactor : SimParameters
proxyTreeNode() : proxyTreeNode
proxyUsage : Rebalancer
ProxyUsage() : ProxyUsage
ProxyUsageKey() : ProxyUsageKey
psiFin : Patch
psiSum : ProxyGBISP1ResultMsg, Patch, GBISParamStruct, ComputeNonbondedCUDA::patch_record
psiSumBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA::patch_record
psiSumBoxClosed() : Patch
psiSumComputeList : Patch
psiSumH : ComputeNonbondedCUDA
psiSumLen : ProxyGBISP1ResultMsg
publish() : SimpleBroadcastObject< T >
pup() : Pointer, MoaData, Int3, Int2, HashPoolAdaptorT< T >
push_back() : HashPool< T >
put() : MOStream, MsmC1HermiteGridCutoffSetupMsg, MsmGridCutoffSetupMsg, MsmC1HermiteGridCutoffProxyMsg, MsmGridCutoffProxyMsg, MsmC1HermiteBlockProxyMsg, MsmBlockProxyMsg, GridMsg
put_stir_startTheta() : Molecule

- q -

q : CudaAtom, colvarmodule::rotation
q0 : colvarmodule::quaternion
q1 : colvarmodule::quaternion
q2 : colvarmodule::quaternion
q3 : colvarmodule::quaternion
q_old : colvarmodule::rotation
qgrid : OptPmeFFTMsg, OptPmeGridMsg, PmeUntransMsg, PmeTransMsg, PmeGridMsg
qh : NL_Msm_t, MsmBlockKernel< Vtype, Mtype >, MsmGridCutoffKernel< Vtype, Mtype >, msm::PatchData, MoaData
qh_c1hermite : msm::PatchData
qh_f : NL_Msm_t
qhblockIndex : MsmGridCutoffKernel< Vtype, Mtype >
qhBlockIndex : MsmGridCutoffInitMsg
qhRestricted : MsmBlockKernel< Vtype, Mtype >
qq : thole
quaternion() : colvarmodule::quaternion
quaternion_value : colvarvalue
quenchVelocities() : Sequencer
queue : CollectionMaster::CollectVectorSequence
QUINTIC : ComputeMsmMgr
QUINTIC2 : ComputeMsmMgr

- r -

r : doublecomplex, ComputePatchPair, ComputePatch, ComputeNonbondedCUDA::patch_record, LCPOAtom, TuplePatchElem, PatchElem, floatcomplex
r0 : colvar::h_bond, colvar::selfcoordnum, colvar::coordnum
r0_vec : colvar::coordnum
r12 : colvar::dihedral
r21 : colvar::angle
r21l : colvar::angle
r23 : colvar::dihedral, colvar::angle
r23l : colvar::angle
r2_delta : ComputeNonbondedUtil
r2_delta_1 : ComputeNonbondedUtil
r2_delta_exp : ComputeNonbondedUtil
r2_table : ComputeNonbondedUtil
r2list : ComputeNonbondedWorkArrays
r34 : colvar::dihedral
r_ohc : Molecule
r_om : Molecule
r_ub : AngleValue, angle_params
rand : Node
rand_gaussian() : colvarproxy_namd, colvarproxy, colvarmodule
random : Sequencer, Controller, colvarproxy_namd
Random() : Random, AVector
randomSeed : SimParameters
range : ParseOptions, ParseOptions::DataElement
rankInPhysOfNode : pe_sortop_bit_reversed
rattle1() : Sequencer, HomePatch
rattle2() : Sequencer, HomePatch
read_block() : colvarparse::read_block
read_charmm_parameter_file() : Parameters
read_ener_table() : Parameters
read_energy_type() : Parameters
read_energy_type_bothcubspline() : Parameters
read_energy_type_cubspline() : Parameters
read_fortran_12I6() : parm
read_go_file() : Molecule
read_hill() : colvarbias_meta
read_multicol() : colvar_grid< T >
read_parameter_file() : Parameters
read_parm() : Parameters, Molecule
read_position() : colvarmodule::atom
read_positions() : colvarmodule::atom_group
read_raw() : colvar_grid< T >
read_raw_error() : colvar_grid< T >
read_replica_files() : colvarbias_meta
read_restart() : colvarmodule, colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvarbias_meta, colvarbias_harmonic, colvarbias, colvar
read_system_force() : colvarmodule::atom
read_system_forces() : colvarmodule::atom_group
read_traj() : colvarmodule, colvar
read_velocities() : colvarmodule::atom_group
read_velocity() : colvarmodule::atom
readExclusions : SimParameters
readHeader() : GridforceFullBaseGrid
readparm() : parm
readPerAtomInfo() : ParallelIOMgr
readSubgridHierarchy() : GridforceFullBaseGrid
ready() : CollectionMaster::CollectVectorInstance
real : colvarmodule
real_node : NodePmeInfo
real_value : colvarvalue
reassignFreq : SimParameters
reassignHold : SimParameters
reassignIncr : SimParameters
reassignTemp : SimParameters
reassignVelocities() : Sequencer, Controller
rebalance() : LdbCoordinator
rebalanceLoad() : Sequencer, Controller
Rebalancer() : Rebalancer
rebin_grids : colvarbias_meta
RecBisection() : RecBisection
receive_GoMolecule() : Molecule
receive_Molecule() : Molecule
receive_Parameters() : Parameters
receive_SimParameters() : SimParameters
receiveAll() : ProxyPatch
ReceiveAtSync() : LdbCoordinator
receiveData() : ProxyPatch
receiveDataStream() : CollectionMaster
receiveForces() : ParallelIOMgr, CollectionMaster
receiveOutputForceReady() : CollectionMaster
receiveOutputPosReady() : CollectionMaster
receiveOutputVelReady() : CollectionMaster
receivePositions() : ParallelIOMgr, CollectionMaster
receivePressure() : Controller
receiveResult() : HomePatch
receiveResults() : HomePatch
receiveVelocities() : ParallelIOMgr, CollectionMaster
recent_dEdl_elec_1 : Controller
recent_dEdl_elec_2 : Controller
recent_dEdl_lj_1 : Controller
recent_dEdl_lj_2 : Controller
recent_TiNo : Controller
recipvec1 : NL_Msm_t
recipvec1_f : NL_Msm_t
recipvec2 : NL_Msm_t
recipvec2_f : NL_Msm_t
recipvec3 : NL_Msm_t
recipvec3_f : NL_Msm_t
reconfig : ComputeGlobalResultsMsg
recount_hills_off_grid() : colvarbias_meta
recv_ack_idx : DataExchanger
recv_bcast_idx : DataExchanger
recv_data_idx : DataExchanger
recv_grid() : OptPmeZPencil, PmeZPencil
recv_red_idx : DataExchanger
recv_trans() : OptPmeXPencil, OptPmeYPencil, PmeXPencil, PmeYPencil
recv_untrans() : OptPmeYPencil, OptPmeZPencil, PmeYPencil, PmeZPencil
recvAck() : ComputePmeMgr
recvArrays() : OptPmeMgr, ComputePmeMgr
recvAtoms() : PatchMgr
recvAtomsCntPerPatch() : ParallelIOMgr
recvAtomsMGrp() : ParallelIOMgr
recvAtomsToHomePatchProcs() : ParallelIOMgr
recvBroadcast() : BroadcastMgr
recvBuildCudaForceTable() : ComputeMgr
recvClusterCoor() : ParallelIOMgr
recvClusterSize() : ParallelIOMgr
recvComputeConsForceMsg() : ComputeMgr
recvComputeDPMEData() : ComputeMgr
recvComputeDPMEResults() : ComputeMgr
recvComputeEwaldData() : ComputeMgr
recvComputeEwaldResults() : ComputeMgr
recvComputeGlobalConfig() : ComputeMgr
recvComputeGlobalData() : ComputeMgr
recvComputeGlobalResults() : ComputeMgr
recvComputeMapChanges() : WorkDistrib
recvCoord() : ComputeMsmSerialMgr, ComputeGBISserMgr, ComputeFmmSerialMgr, ComputeExtMgr
recvCreateNonbondedCUDASlave() : ComputeMgr
recvData() : ProxyMgr, GlobalMasterServer, ComputeEwald
recvEnableEarlyExit() : Node
recvEnableExitScheduler() : Node
recvEvir() : OptPmeMgr
recvFinalClusterCoor() : ParallelIOMgr
recvFinalClusterSize() : ParallelIOMgr
recvForce() : ComputeMsmSerialMgr, ComputeGBISserMgr, ComputeFmmSerialMgr, ComputeExtMgr
recvGrid() : ComputePmeMgr
recvGridCutoff : msm::BlockDiagram
recvHydroBasedCounter() : ParallelIOMgr
recvImmediateProxyAll() : NodeProxyMgr, ProxyMgr
recvImmediateProxyData() : NodeProxyMgr, ProxyMgr
recvImmediateResults() : NodeProxyMgr, ProxyMgr
RecvMigrate() : LdbCoordinator
recvMigrateAtomsCombined() : PatchMgr
recvMolInfo() : ParallelIOMgr
recvMovePatches() : PatchMgr
recvMsmBlockProxy() : ComputeMsmMgr
recvMsmC1HermiteBlockProxy() : ComputeMsmMgr
recvMsmC1HermiteGridCutoffProxy() : ComputeMsmMgr
recvMsmGridCutoffProxy() : ComputeMsmMgr
recvNodeAwareSpanningTree() : ProxyMgr, HomePatch
recvNodeAwareSpanningTreeOnHomePatch() : ProxyMgr
recvNodeAwareSTParent() : ProxyMgr
recvNonbondedCUDASlaveReady() : ComputeMgr
recvPatchProxyInfo() : ProxyMgr
recvPencilMapProxies() : NodePmeMgr
recvProxies() : ProxyMgr
recvProxyAll() : ProxyMgr
recvProxyData() : ProxyMgr
recvred : DataExchanger
recvRegisterProxy() : ProxyMgr
recvResult() : ProxyMgr
recvResults() : ProxyMgr, ComputeGlobal, ComputeEwald
recvSharedTrans() : ComputePmeMgr
recvSharedUntrans() : ComputePmeMgr
recvSpanningTree() : ProxyMgr, HomePatch
recvSpanningTreeOnHomePatch() : ProxyMgr
recvTrans() : NodePmeMgr, ComputePmeMgr
recvUngrid() : OptPmeMgr, ComputePmeMgr
recvUnregisterProxy() : ProxyMgr
recvUntrans() : NodePmeMgr, ComputePmeMgr
recvXTrans() : NodePmeMgr
recvYieldDevice() : ComputeNonbondedCUDA, ComputeMgr
recvYTrans() : NodePmeMgr
recvYUntrans() : NodePmeMgr
recvZGrid() : NodePmeMgr
recvZUntrans() : NodePmeMgr
reduction : Sequencer, OptPmeXPencil, Controller, ComputeStir, ComputeSphericalBC, ComputeRestraints, nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeNonbondedCUDA, ComputeLCPO, ComputeHomeTuples< T, S, P >, ComputeGridForce, ComputeEField, ComputeCylindricalBC, colvarproxy_namd
reductionChecksumLabel : TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
reductionData : ComputeNonbondedSelf, ComputeNonbondedPair, ComputeLCPO
reductionDataSize : TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
ReductionMgr : ReductionMgr, RequireReduction, SubmitReduction
reductionMgr : BOCgroup
ReductionSet() : ReductionSet
ReductionSetData() : ReductionSetData
reductionSetID : ReductionSet, ReductionSubmitMsg, ReductionRegisterMsg
ref1 : colvar::distance_z
ref2 : colvar::distance_z
ref_pos : colvar::rmsd, colvar::orientation, colvar::eigenvector, colvarmodule::atom_group
ref_pos_center : colvar::eigenvector
ref_pos_cog : colvarmodule::atom_group
ref_pos_group : colvarmodule::atom_group
ref_quat : colvar::orientation
refCount : UniqueSetRaw< Elem >, ComputeNonbondedCUDA::patch_record
refine() : Rebalancer
refine_togrid() : Rebalancer
RefineOnly() : RefineOnly
RefineTorusLB() : RefineTorusLB
reg_all_objs : LdbCoordinator
registerArray() : PmePencilMap, MsmGridCutoffMap, MsmBlockMap
registerAvgPositionPickup() : Patch
registerBornRadPickup() : Patch
registerCompute() : ComputeMap
registerDEdaSumDeposit() : Patch
registerDHdrPrefixPickup() : Patch
registerForceDeposit() : Patch
registerIDsCompAtomExt() : AtomMapper
registerIDsFullAtom() : AtomMapper
registerIntRadPickup() : Patch
registerLcpoTypePickup() : Patch
registerLocalPatchMap() : NodeProxyMgr
registerLocalProxyMgr() : NodeProxyMgr
registerPatch() : NodeProxyMgr, PatchMap
registerPatches() : ComputeNonbondedCUDA
registerPatchMgr() : PatchMap
registerPositionPickup() : Patch
registerProxy() : ProxyMgr, HomePatch
registerPsiSumDeposit() : Patch
registerVelocityPickup() : Patch
registerXPencil() : NodePmeMgr
registerYPencil() : NodePmeMgr
registerZPencil() : NodePmeMgr
rehash() : UniqueSetRaw< Elem >, UniqueSet< Elem >
reinitAtoms() : WorkDistrib
reinitialize() : GridforceLiteGrid, GridforceFullMainGrid, GridforceGrid
reinitVelocities() : Sequencer
reloadCharges() : Sequencer, Node, Molecule
reloadGridforceGrid() : Node
REMARK : PDBData
remoteActivePatches : ComputeNonbondedCUDA
remoteComputeRecords : ComputeNonbondedCUDA
remoteHostedPatches : ComputeNonbondedCUDA
remoteRegister() : ReductionMgr
remoteSubmit() : ReductionMgr
remoteUnregister() : ReductionMgr
remove() : IRSet, msm::PriorityQueue< T >
removeData() : ReductionSet
removeEmptyOffset() : ExclusionSignature
removeEmptyTupleSigs() : AtomSignature
removeProxies() : ProxyMgr
removeProxy() : ProxyMgr
removeReady() : CollectionMaster::CollectVectorSequence
removeSelf() : Entry< Elem >
removeUnusedProxies() : ProxyMgr
reorder() : Random
rep : ResizeArray< Elem >
replace : ExtForce
replaceForces() : HomePatch
replica : colvarbias_meta::hill
replica_file_name : colvarbias_meta
replica_hills_file : colvarbias_meta
replica_hills_file_pos : colvarbias_meta
replica_hills_os : colvarbias_meta
replica_id : colvarbias_meta
replica_list_file : colvarbias_meta
replica_state_file : colvarbias_meta
replica_state_file_in_sync : colvarbias_meta
replica_update_freq : colvarbias_meta
replicas : colvarbias_meta
replicas_registry : colvarbias_meta
replicas_registry_file : colvarbias_meta
report_timings : NL_Msm_t
Req : parm
reqAtoms : GlobalMaster
reqAtomsChanged : GlobalMaster
reqGroups : GlobalMaster
reqGroupsChanged : GlobalMaster
request_group1_gradients() : colvarmodule::rotation
request_group2_gradients() : colvarmodule::rotation
request_system_force() : colvarproxy_namd, colvarproxy, colvarmodule
requestAtom() : GlobalMasterFreeEnergy, GlobalMasterEasy
requestedAtoms() : GlobalMaster
requestedGroups() : GlobalMaster
require() : RequireReduction, ParseOptions
requireB() : ParseOptions
requiredProxies() : LdbCoordinator
requirePatch() : ComputeNonbondedCUDA
RequireReduction : ReductionMgr
requireRegistered : ReductionSet
rescale() : Lattice
rescaleaccelMD() : Sequencer, Controller
rescaleFreq : SimParameters
rescaleTemp : SimParameters
rescaleVelocities() : Sequencer, Controller
rescaleVelocities_numTemps : Sequencer, Controller
rescaleVelocities_sumTemps : Controller
rescaleVelocitiesByFactor() : Sequencer
resendCoordinates : ComputeGlobalResultsMsg
reset() : Rebalancer::pcpair, msm::BlockDiagram, msm::PatchDiagram, msm::PatchSend, msm::BlockSend, msm::Grid< T >, msm::GridFixed< T, N >, msm::Array< T >, Pairlists, LCPONeighborList, colvarvalue, colvarmodule::quaternion, colvarmodule::matrix2d< T, outer_length, inner_length >, colvarmodule::vector1d< T, length >, colvarmodule::rvector, colvar_grid< T >, CollectionMgr::CollectVectorInstance, CollectionMaster::CollectVectorInstance
reset_atoms_data() : colvarmodule::atom_group
reset_bias_force() : colvar
reset_data() : colvarmodule::atom
reset_rotation() : colvarmodule::quaternion
resid : seg_resid
resID : OutputAtomRecord::integerVals, BasicAtomInfo
residue_id : colvarmodule
ResidueLookupElem() : ResidueLookupElem
residuename() : PDBAtom
residueseq() : PDBAtom
resize() : ResizeArray< Elem >, msm::Grid< T >, msm::Array< T >
ResizeArray() : ResizeArray< Elem >
ResizeArray<Elem> : ResizeArrayRaw< Elem >
ResizeArrayIter() : ResizeArrayIter< T >
ResizeArrayIter<Elem> : ResizeArrayRaw< Elem >, ResizeArray< Elem >
ResizeArrayPrimIter() : ResizeArrayPrimIter< T >
resname : atom_name_info
resnameIdx : AtomNameIdx
resNameIdx : OutputAtomRecord::shortVals, BasicAtomInfo
ResNames : parm
resStencil : MsmBlockKernel< Vtype, Mtype >
restart_frequency() : colvarproxy_namd, colvarproxy
restart_frequency_s : colvarproxy_namd
restart_in_name : colvarmodule
restart_out_freq : colvarmodule
restart_out_name : colvarmodule
restart_out_os : colvarmodule
restart_output_prefix() : colvarproxy_namd, colvarproxy
restart_output_prefix_str : colvarproxy_namd
restartFilename : SimParameters
restartFrequency : SimParameters
restartSave : SimParameters
restraint_FE : colvarbias_harmonic
RESTRICT : MsmTimer
restriction() : MsmC1HermiteBlock, MsmBlock
restrictionKernel() : MsmBlockKernel< Vtype, Mtype >
restrictions : go_val
results : Patch
resume() : LdbCoordinator
resume2() : LdbCoordinator
resumeAfterPapiMeasureBarrier() : Node
resumeAfterTraceBarrier() : Node, Controller
ResumeFromSync() : LdbCoordinator
resumeReady() : LdbCoordinator
REVDAT : PDBData
reverse_transform() : Lattice
revert() : HomePatch
rho : ComputeGBISAtom
rho0 : ComputeGBISAtom
rho_0 : GBISParamStruct
rhos : ComputeGBISAtom
right : indexed_table_pair, indexed_nbthole_pair, indexed_vdw_pair, vdw_params, angle_params, bond_params
rigid_bond_length() : Molecule
rigidBondLength : FullAtom, OutputAtomRecord::floatVals
rigidBonds : SimParameters
rigidDie : SimParameters
rigidIter : SimParameters
rigidTol : SimParameters
Rk : parm
rlength() : Vector
rmatrix() : colvarmodule::rmatrix
rmsd() : colvar::rmsd
rot : Matrix4, colvar::orientation, colvarmodule::atom_group
rotate() : colvarmodule::rotation, colvarmodule::quaternion
rotate_axis() : Matrix4
rotation() : colvarmodule::rotation
rotation_matrix() : colvarmodule::quaternion
rotConsAxis : SimParameters
rotConsPivot : SimParameters
rotConstraintsOn : SimParameters
rotConsVel : SimParameters
rotDragAxisFile : SimParameters
rotDragFile : SimParameters
rotDragGlobVel : SimParameters
rotDragOn : SimParameters
rotDragPivotFile : SimParameters
rotDragVelFile : SimParameters
rowsize : Parameters, ComputeNonbondedUtil
ru : ComputeMsmMgr
run() : Sequencer, ScriptTcl, Node, Controller
runave : colvar
runave_length : colvar
runave_os : colvar
runave_stride : colvar
runave_variance : colvar
runComputeObjects() : Sequencer
runController() : NamdState
runSequencer() : HomePatch
rv : ComputeMsmMgr
rvector() : colvarmodule::rvector
rvector_value : colvarvalue
rw : ComputeMsmMgr

- s -

s_edge : ComputeMsmMgr
safely_read_restart : colvarbias_meta
SALT : PDBAtom
samples : colvar_grid_gradient, colvar_grid_scalar
save_delimiters : colvarparse
saveComputeMap() : WorkDistrib, ComputeMap
saveComputeMapChanges() : WorkDistrib
saveForce() : Sequencer, HomePatch
saveMolDataPointers() : Node
savePairlists : Flags, nonbonded
savePatchMap() : WorkDistrib
saveResults() : ComputeMsmSerial, ComputeMsm, ComputeGBISser, ComputeFmmSerial, ComputeExt
saveTotalForces() : ComputeGlobal
Scale() : AVector
scale : Matrix4, Lattice, colvarbias_meta::hill, GridforceLiteGrid, GridforceFullBaseGrid, TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
SCALE : PDBData
scale14 : SimParameters, ComputeNonbondedUtil
scale_d2V : GridforceFullSubGrid
scale_d3V : GridforceFullSubGrid
scale_dV : GridforceFullSubGrid
scaling : ComputeNonbondedUtil
scan() : PDBData
SCHAIN : PDBAtom
scor_table : ComputeNonbondedUtil
scriptArg1 : SimParameters
scriptArg2 : SimParameters
scriptArg3 : SimParameters
scriptArg4 : SimParameters
scriptArg5 : SimParameters
scriptBarrier : Node, ControllerBroadcasts
scriptParam() : Node
scriptSet() : SimParameters
ScriptTcl : ScriptTcl, NamdState, Controller
segmentname() : PDBAtom
segname : seg_resid
segNameIdx : OutputAtomRecord::shortVals, BasicAtomInfo
select() : ComputeNonbondedUtil
select_closest_image() : colvarproxy_namd, colvarproxy, colvarmodule
select_closest_images() : colvarproxy, colvarmodule
selectConstraintsOn : SimParameters
SELEMENT : PDBAtom
selfcoordnum() : colvar::selfcoordnum
send : BroadcastMgr, msm::PatchDiagram
send_all_ungrid() : PmeZPencil
send_energies() : GlobalMasterIMD
send_fcoords() : GlobalMasterIMD
send_GoMolecule() : Molecule
send_Molecule() : Molecule
send_order : OptPmePencil< T >, PmePencil< T >
send_Parameters() : Parameters
send_SimParameters() : SimParameters
send_subset_trans() : PmeYPencil, PmeZPencil
send_subset_ungrid() : PmeZPencil
send_subset_untrans() : PmeXPencil, PmeYPencil
send_trans() : OptPmeYPencil, OptPmeZPencil, PmeYPencil, PmeZPencil
send_ungrid() : OptPmeZPencil, PmeZPencil
send_untrans() : OptPmeXPencil, OptPmeYPencil, PmeXPencil, PmeYPencil
sendAcross : msm::BlockDiagram
sendAtoms() : PatchMgr
sendAtomsThread : ParallelIOMgr
sendAtomsToHomePatchProcs() : ParallelIOMgr
sendbcast : DataExchanger
sendBuildCudaForceTable() : ComputeMgr
sendCharge() : msm::PatchData
sendChargeC1Hermite() : msm::PatchData
sendComputeDPMEData() : ComputeMgr
sendComputeDPMEResults() : ComputeMgr
sendComputeEwaldData() : ComputeMgr
sendComputeEwaldResults() : ComputeMgr
sendComputeGlobalConfig() : ComputeMgr
sendComputeGlobalData() : ComputeMgr
sendComputeGlobalResults() : ComputeMgr
sendComputeMap() : WorkDistrib
sendCreateNonbondedCUDASlave() : ComputeMgr
sendData() : ComputePmeMgr
sendDataStream() : CollectionMgr
sendDown : msm::BlockDiagram
sendDownPotential() : MsmC1HermiteBlock, MsmBlock
sendEnableEarlyExit() : Node
sendEnableExitScheduler() : Node
sendMessage() : Communicate
sendMigrationMsgs() : PatchMgr
sendMovePatches() : PatchMgr
sendNodeAwareSpanningTree() : ProxyMgr, HomePatch
sendNodeAwareSpanningTreeToHomePatch() : ProxyMgr
sendNonbondedCUDASlaveEnqueue() : ComputeMgr
sendNonbondedCUDASlaveReady() : ComputeMgr
sendOneHomePatch() : PatchMgr
sendPatch : MsmC1HermiteBlock, MsmBlock, msm::BlockDiagram
sendPatchMap() : WorkDistrib
sendPencils() : OptPmeCompute, ComputePmeMgr
sendProxies() : ProxyMgr, HomePatch
sendProxyAll() : ProxyMgr
sendProxyData() : ProxyMgr
sendProxyList() : NodeProxyMgr
sendProxyListInfo() : NodeProxyMgr
sendResult() : ProxyMgr
sendResults() : ProxyMgr
sendSpanningTree() : ProxyMgr, HomePatch
sendSpanningTrees() : ProxyMgr
sendSpanningTreeToHomePatch() : ProxyMgr
sendTrans() : ComputePmeMgr
sendTransBarrier() : ComputePmeMgr
sendUngrid() : ComputePmeMgr
sendUntrans() : ComputePmeMgr
sendUp : msm::BlockDiagram
sendUpCharge() : MsmC1HermiteBlock, MsmBlock
sendYieldDevice() : ComputeMgr
SEPTIC : ComputeMsmMgr
SEPTIC3 : ComputeMsmMgr
seq : CollectionMgr::CollectVectorInstance, CollectVectorVarMsg, CollectionMaster::CollectVectorInstance, CollectVectorMsg
seqnum : GridMsg
SEQRES : PDBData
sequence : Compute, Flags, PmePencil< T >, PmeTransMsg, PmeGridMsg, GBISParamStruct, MsmBlockKernel< Vtype, Mtype >, MsmGridCutoffKernel< Vtype, Mtype >, msm::PatchData, GBISCoordMsg
sequenceNumber : ReductionSetData, ReductionSubmitMsg
Sequencer : Sequencer, HomePatch
sequencerThreads : LdbCoordinator
serialnumber() : PDBAtom
set() : Vector, ParseOptions, msm::FoldFactor, msm::Grid< T >, msm::GridFixed< T, N >, msm::IndexRange, C1Matrix, C1Vector, Lattice, colvarmodule::quaternion, colvarmodule::rvector
Set() : AVector
set_all_gridvals() : GridforceLiteGrid, GridforceFullMainGrid, GridforceGrid
set_all_positions() : PDB
set_from_euler_angles() : colvarmodule::quaternion
set_grid() : GridforceLiteGrid, GridforceFullBaseGrid
set_gridfrc_grid() : Molecule
set_num_atoms() : PmeRealSpace
set_positive() : colvarmodule::quaternion
set_sizes() : colvar_grid< T >
set_transrate() : IMDOutput
set_value() : colvar_grid< T >
set_weighted_gradient() : colvarmodule::atom_group
setall() : ResizeArray< Elem >
setBFactorData() : Molecule
setBlockSize() : ObjectArena< Type >
SetBound() : ABoundAngleRestraint, ABoundDistRestraint, ABoundPosRestraint, ARestraint
setbounds() : msm::Grid< T >, msm::GridFixed< T, N >, msm::IndexRange
setCompute() : OptPmeMgr, ComputeMsmSerialMgr, ComputeMsmMgr, ComputeGBISserMgr, ComputeFmmSerialMgr, ComputeExtMgr
setEmpty() : TupleSignature
SetEqual : AVector
setGBISIntrinsicRadii() : HomePatch
SetGroup() : ARestraint
SetGroups() : ARestraint
setHomePatchFixedAtomNum() : PatchMgr
setIndexValue() : Pairlists
SetIntervalAngle() : ABoundDiheRestraint, ARestraint
SetKf() : ARestraint
SetLambdaKf() : ARestraintManager, ARestraint, ALambdaControl
SetLambdaRef() : ARestraintManager, ARestraint, ALambdaControl
SetLambdas() : ARestraintManager
setLattice() : PatchMgr
setLcpoType() : HomePatch
SetLowerAngle() : ABoundDiheRestraint, ARestraint
setmax() : msm::Array< T >
setMessage() : DataMessage
setMgr() : OptPmeCompute, ComputePme, ComputeMsm
setNewNode() : ComputeMap
setNewNumPartitions() : ComputeMap
setNext() : EntryGlob< Elem >, Entry< Elem >
setNode() : ComputeMap
SetNumAccumSteps() : ALambdaControl
SetNumEquilSteps() : ALambdaControl
setNumFixedAtoms() : Patch
setNumPartitions() : ComputeMap
setNumPatches() : Compute
SetNumPrintSteps() : ALambdaControl
SetNumRepeats() : ALambdaControl
SetNumSteps() : ALambdaControl
setOccupancyData() : Molecule
setOffsets() : ExclusionSignature, TupleSignature
setPatchMapArrived() : WorkDistrib
setPlugin() : PluginIOMgr
setProxyTreeBranchFactor() : ProxyMgr
setRecvSpanning() : ProxyMgr
SetRefAngle() : AFixedDiheRestraint, ABoundAngleRestraint, AFixedAngleRestraint, ARestraint
SetRefDist() : ABoundDistRestraint, AFixedDistRestraint, ABoundPosRestraint, ARestraint
SetRefPos() : ABoundPosRestraint, AFixedPosRestraint, ARestraint
setSafeNoDestruction() : UniqueSetRaw< Elem >
setScript() : Node
setSendSpanning() : ProxyMgr
setSpanningTree() : ProxyPatch
SetStartAngle() : AForcingDiheRestraint, AForcingAngleRestraint, ARestraint
SetStartDist() : AForcingDistRestraint, ARestraint
SetStartPos() : AForcingPosRestraint, ARestraint
SetStartStep() : ALambdaControl
SetStopAngle() : AForcingDiheRestraint, AForcingAngleRestraint, ARestraint
SetStopDist() : AForcingDistRestraint, ARestraint
SetStopPos() : AForcingPosRestraint, ARestraint
SetStopStep() : ALambdaControl
SetTask() : ALambdaControl
setup() : MsmC1HermiteGridCutoff, MsmGridCutoff, MsmGridCutoffKernel< Vtype, Mtype >
setup_hgrid_1d() : ComputeMsmMgr
setup_periodic_blocksize() : ComputeMsmMgr
SetUpperAngle() : ABoundDiheRestraint, ARestraint
setupSections() : MsmC1HermiteBlock, MsmBlock, MsmC1HermiteGridCutoff, MsmGridCutoff
setupStencils() : MsmBlockKernel< Vtype, Mtype >
setupWeights() : MsmGridCutoffKernel< Vtype, Mtype >
SFOOT : PDBAtom
sglower : ComputeMsmMgr
sh : MoaData
shared() : ResizeArray< Elem >
SHEET : PDBData
shx : ComputeMsmMgr
shx_1 : ComputeMsmMgr
shy : ComputeMsmMgr
shy_1 : ComputeMsmMgr
shz : ComputeMsmMgr
shz_1 : ComputeMsmMgr
SIGATM : PDBData
sigma : vdw_val, vdw_params
sigma14 : vdw_val, vdw_params
sigmaRep : go_val
sign() : ComputeMsmMgr
SIGUIJ : PDBData
SimParameters() : SimParameters
simParameters : Node
simparams : colvarproxy_namd
simParams : Sequencer, Controller
SimpleBroadcastObject() : SimpleBroadcastObject< T >
simulatedNodeSize : SimParameters
simulatedPEs : SimParameters
simulateInitialMapping : SimParameters
single_pencil : OptPmePencil< T >
single_replica : colvarbias_meta
SINSERT : PDBAtom
SITE : PDBData
size : UniqueSetRaw< Elem >, UniqueSet< Elem >, ResizeArray< Elem >, DihedralTable, AngleTable, BondTable, AtomTable, HashPool< T >, colvarmodule::vector1d< T, length >, GridforceLiteGrid, GridforceFullBaseGrid, DataMessage, TholeElem, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem, CollectVectorVarMsg
size_nopad : GridforceFullBaseGrid
sizeGrid() : PatchMap
sizeList : MovePatchAtomsMsg
sizes : colvar_grid< T >, ProxyTree
skip() : Random, Box< Owner, Data >
skipWork() : LdbCoordinator
slaveIndex : ComputeNonbondedCUDA
slavePes : ComputeNonbondedCUDA
slaves : ComputeNonbondedCUDA
sldata : ParseOptions::DataElement
slow : Results
slow_forces : ComputeNonbondedCUDA
slow_table : ComputeNonbondedUtil
slowForce : GBISForceMsg
slowFreq : Sequencer, Controller
slowVirialIndex : ExclElem
slptr : ParseOptions::DataElement
smax : MsmInitMsg, ComputeMsmMgr
SMDDir : SimParameters
SMDFile : SimParameters
SMDk : SimParameters
SMDk2 : SimParameters
SMDOn : SimParameters
SMDOutputFreq : SimParameters
SMDVel : SimParameters
smin : MsmInitMsg, ComputeMsmMgr
smooth2_avg : Controller
smooth2_avg2 : Controller
SNAME : PDBAtom
SOCC : PDBAtom
sock : GlobalMasterIMD
Solty : parm
solvent_dielectric : SimParameters
sort() : SortedArray< Elem >, SortableResizeArray< Elem >
SortableResizeArray() : SortableResizeArray< Elem >
SortableResizeArray<Elem> : ResizeArrayRaw< Elem >
sorted_ids : colvarmodule::atom_group
SortedArray() : SortedArray< Elem >
SortedArray<Elem> : ResizeArrayRaw< Elem >
sortExclOffset() : ExclSigInfo
sortop_base() : sortop_base
sortop_x() : sortop_x
sortop_y() : sortop_y
sortop_z() : sortop_z
sortOrder : CompAtomExt
sortPmePes() : WorkDistrib
sortTupleSigIndices() : AtomSigInfo
sortValue : __sort_entry
SOURCE : PDBData
sourceNode : ReductionSubmitMsg, ReductionRegisterMsg, OptPmeFFTMsg, OptPmeGridMsg, PmeUntransMsg, PmeTransMsg, PmeGridMsg, MsmSerialCoordMsg, GBISCoordMsg, FmmSerialCoordMsg, ExtCoordMsg
sp_zstorage : OptPmeCompute
specialTracing : Node
sphericalBCexp1 : SimParameters
sphericalBCexp2 : SimParameters
sphericalBCk1 : SimParameters
sphericalBCk2 : SimParameters
sphericalBCOn : SimParameters
sphericalBCr1 : SimParameters
sphericalBCr2 : SimParameters
sphericalCenter : SimParameters
sphericalConstraintsOn : SimParameters
sphericalConstrCenter : SimParameters
spin_angle() : colvarmodule::rotation, colvar::spin_angle
split : Random, NL_Msm_t, ComputeMsmMgr
Split : ComputeMsmMgr
splitComputes() : ComputeMgr
splitComputes2() : ComputeMgr
splitPatch : SimParameters
splitting() : ComputeMsmMgr
spos : pe_sortop_coord_y, pe_sortop_coord_x
sprint() : PDBAtom, PDBUnknown, PDBData
sprintcol() : PDBData
SPRSDE : PDBData
sptr : ParseOptions::DataElement
square() : ComputeNonbondedUtil
src : DataMessage
src_pe : OptPmeSubComputeMsg
srcPart : DataMessage
srcPatchID : MigrateAtomsCombinedMsg, MigrateAtomsMsg
srcRank : ClusterCoorMsg, ClusterSizeMsg
SRESNAME : PDBAtom
SRESSEQ : PDBAtom
srx_x : ComputeMsmMgr
srx_y : ComputeMsmMgr
srx_z : ComputeMsmMgr
sry_x : ComputeMsmMgr
sry_y : ComputeMsmMgr
sry_z : ComputeMsmMgr
srz_x : ComputeMsmMgr
srz_y : ComputeMsmMgr
srz_z : ComputeMsmMgr
SSBOND : PDBData
SSEGNAME : PDBAtom
SSERIAL : PDBAtom
sSet : OutputAtomRecord
stage : colvarbias_harmonic
star() : floatcomplex
Start : PDBAtom
start : OptPmeSubComputeMsg, PmeGridMsg
startHPM() : Node
starting_force_k : colvarbias_harmonic
startNextRoundOutputForce() : CollectionMaster
startNextRoundOutputPos() : CollectionMaster
startNextRoundOutputVel() : CollectionMaster
startPE : LocalLBInfoMsg
startup() : Node
startUp() : Node
startWork() : LdbCoordinator
state : Node, Controller
state_file_step : colvarbias_meta
staticAtomAssignment : SimParameters
staticCompare() : ProxyUsageKey, HashPoolAdaptorT< T >
staticHash() : ProxyUsageKey, HashPoolAdaptorT< T >
staticMigrateFn() : LdbCoordinator
staticQueryEstLoadFn() : LdbCoordinator
staticReceiveAtSync() : LdbCoordinator
staticResumeFromSync() : LdbCoordinator
staticStatsFn() : LdbCoordinator
statsOn : SimParameters
status : UniqueSetIter< T >, NamdState, AtomCstInfo, atom_constants, FullAtom, CollectVectorVarMsg
STEMPF : PDBAtom
stencil : InterpParams_t
stencil_1d() : ComputeMsmMgr
stencil_1d_c1hermite() : ComputeMsmMgr
step : Flags, GlobalMaster, ComputeNonbondedCUDA, ComputeLCPO, ComputeGlobalDataMsg
step_absolute() : colvarmodule
step_relative() : colvarmodule
stepsPerCycle : SimParameters
stepsPerLdbCycle : LdbCoordinator
stirAxis : SimParameters
stirFilename : SimParameters
stirK : SimParameters
stirOn : SimParameters
stirPivot : SimParameters
stirStartingTheta : SimParameters
stirVel : SimParameters
stopHPM() : Node
storeCompute() : ComputeMap
storeComputeMap : SimParameters
strainRate : SimParameters
strainRate2 : SimParameters
strainRate_old : Controller
Strategy() : NamdCentLB
strategy() : Rebalancer
strategyName : Rebalancer
STRING : ParseOptions::DataElement
StringList() : StringList
STRINGLIST : ParseOptions::DataElement
strip_values() : colvarparse
STYPE : PDBAtom
subcube_total : NL_Msm_t
subgrid : MsmBlockKernel< Vtype, Mtype >, msm::PatchData, ComputeMsmMgr
subgrid_c1hermite : msm::PatchData, ComputeMsmMgr
subgridIdx : GridforceFullSubGrid
subgrids : GridforceFullBaseGrid
subgrids_flat : GridforceFullMainGrid
submit() : SubmitReduction
submit_evir() : OptPmeXPencil
submitCollections() : Sequencer
submitData() : CollectionMgr::CollectVectorSequence, CollectionMaster::CollectVectorSequence
submitForces() : CollectionMgr
submitHalfstep() : Sequencer
submitLoadStats : HomePatch, Flags
submitMinimizeReductions() : Sequencer
submitMomentum() : Sequencer
submitPositions() : CollectionMgr
submitPressureProfileData() : ComputeNonbondedUtil
SubmitReduction : ReductionMgr
submitReductionData() : TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
submitReductions() : Sequencer, ComputePmeMgr
submitsRecorded : ReductionSetData
submitsRegistered : ReductionSet
submitVelocities() : CollectionMgr
subscribe() : BroadcastMgr
subtractVirialContrib() : ComputeMsmMgr
Sum_dU_dLambdas() : ARestraintManager
sumReducedPotential() : MsmC1HermiteBlock, MsmBlock
sup_coeff : colvar::cvc
sup_np : colvar::cvc
surface_tension : SimParameters
surfaceTensionTarget : SimParameters
suspend() : Sequencer, BackEnd
suspended : BroadcastClient
suspendFor() : BroadcastClient
suspiciousAlchBonds : Molecule
sW : colvarbias_meta::hill
swap : ResizeArray< Elem >, msm::Array< T >
switching_function() : colvar::selfcoordnum, colvar::coordnum
switchingActive : SimParameters
switchingDist : SimParameters
switchOn : ComputeNonbondedUtil
switchOn2 : ComputeNonbondedUtil
switchOn_1 : ComputeNonbondedUtil
SX : PDBAtom
sx_shx : ComputeMsmMgr
SY : PDBAtom
sy_shy : ComputeMsmMgr
symmetric() : Tensor
symmetryFile : SimParameters
symmetryFirstFullStep : SimParameters
symmetryFirstStep : SimParameters
symmetryk : SimParameters
symmetrykfile : SimParameters
symmetryLastFullStep : SimParameters
symmetryLastStep : SimParameters
symmetryMatrixFile : SimParameters
symmetryOn : SimParameters
symmetryScaleForces : SimParameters
Sync() : Sync
sync : BOCgroup
system_force : colvar::cvc, colvarmodule::atom_group, colvar, colvarmodule::atom
system_force_requested : colvarproxy_namd
system_forces() : colvarmodule::atom_group
SZ : PDBAtom
sz_shz : ComputeMsmMgr

- t -

T : IMDEnergies
tab_pair_tree : Parameters
table_alloc : ComputeNonbondedUtil
table_ener : Parameters, ComputeNonbondedUtil
table_noshort : ComputeNonbondedUtil
table_row() : LJTable
table_short : ComputeNonbondedUtil
table_val() : LJTable
table_val_scale14() : LJTable
tableInterpType : SimParameters
tableMaxDist : SimParameters
tablenumtypes : Parameters
tableNumTypes : SimParameters
tableSpacing : SimParameters
tabulatedEnergies : SimParameters
tabulatedEnergiesFile : SimParameters
tag : StreamMessage, TaggedMsg
taggedMsg : BOID
TaggedMsg() : TaggedMsg
tail_corr_ener : Molecule
tail_corr_virial : Molecule
takingLdbData : LdbCoordinator
target_centers : colvarbias_harmonic
target_equil_steps : colvarbias_harmonic
target_force_k : colvarbias_harmonic
target_nstages : colvarbias_harmonic
target_nsteps : colvarbias_harmonic
task : colvar
task_collect_gradients : colvar
task_corrfunc : colvar
task_extended_lagrangian : colvar
task_fdiff_velocity : colvar
task_gradients : colvar
task_grid : colvar
task_Jacobian_force : colvar
task_langevin : colvar
task_lower_boundary : colvar
task_lower_wall : colvar
task_ntot : colvar
task_output_applied_force : colvar
task_output_energy : colvar
task_output_system_force : colvar
task_output_value : colvar
task_output_velocity : colvar
task_report_Jacobian_force : colvar
task_runave : colvar
task_system_force : colvar
task_upper_boundary : colvar
task_upper_wall : colvar
tasks : colvar
tavg_count : Controller
TAYLOR2 : ComputeMsmMgr
TAYLOR2_DISP : ComputeMsmMgr
TAYLOR3 : ComputeMsmMgr
TAYLOR3_DISP : ComputeMsmMgr
TAYLOR4 : ComputeMsmMgr
TAYLOR4_DISP : ComputeMsmMgr
TAYLOR5 : ComputeMsmMgr
TAYLOR5_DISP : ComputeMsmMgr
TAYLOR6 : ComputeMsmMgr
TAYLOR6_DISP : ComputeMsmMgr
TAYLOR7 : ComputeMsmMgr
TAYLOR7_DISP : ComputeMsmMgr
TAYLOR8 : ComputeMsmMgr
TAYLOR8_DISP : ComputeMsmMgr
tclBCArgs : SimParameters
tclBCOn : SimParameters
tclBCScript : SimParameters
tclForcesOn : SimParameters
tclIsThreaded : SimParameters
tcoupleCoefficient : ControllerBroadcasts
tCoupleOn : SimParameters
tCoupleTemp : SimParameters
tcoupleVelocities() : Sequencer, Controller
temp_avg : Controller
temperature : colvarproxy_namd, colvarproxy, colvarmodule, Controller
temperaturefactor() : PDBAtom
Tensor() : Tensor
tensorMult() : GridforceFullSubGrid
Teq : parm
TER : PDBData
terminate() : Sequencer, Controller
testOn : SimParameters
tf : ComputeGlobalDataMsg
theLbdb : LdbCoordinator
ThereIsAForcingRestraint() : ARestraintManager
thermostat_temperature : colvarproxy_namd
theta : colvar::dihedPC, colvar::alpha_angles
theta0 : AngleValue
theta_ref : colvar::alpha_angles
theta_tol : colvar::alpha_angles
thole : drude_constants
TholeElem : TholeElem, Molecule
tholeEnergyIndex : TholeElem
tholeij : nbthole_pair_value, indexed_nbthole_pair, nbthole_pair_params
thread : BroadcastClient
threadIsWaiting : ReductionSet
tiFile : Controller
tilt() : colvar::tilt
timer : wkfmsgtimer, NL_Msm_t
timer_longrng : NL_Msm_t
timing : MsmTimer
TiNo : Controller
Tk : parm
TMDDiffRMSD : SimParameters
TMDFile : SimParameters
TMDFile2 : SimParameters
TMDFinalRMSD : SimParameters
TMDFirstStep : SimParameters
TMDInitialRMSD : SimParameters
TMDk : SimParameters
TMDLastStep : SimParameters
TMDOn : SimParameters
TMDOutputFreq : SimParameters
to : LdbMigrateMsg
to_lower_cppstr() : colvarparse
to_pe : OptPmeDummyMsg
to_str() : colvarmodule
toRaw() : ProxyCombinedResultMsg
TorusLB() : TorusLB
total_forces : colvarproxy_namd
total_mass : colvarmodule::atom_group
totalAtoms : SimParameters, MigrateAtomsCombinedMsg
totalCharge : MolInfoMsg
totalEnergy : Controller
totalForceBegin : GlobalMaster
totalGrids : GridforceFullMainGrid
totalMass : MolInfoMsg
totalMV : MolInfoMsg
totalStepsDone : LdbCoordinator
trace : Tensor
traceBarrier : Sequencer, Node, Controller, ControllerBroadcasts
traceStartStep : SimParameters
trans : ComputeMap, ComputePatchPair, ComputeMap::PatchRec, ComputeLCPO
Transform() : Transform
transform : FullAtom
translate() : Matrix4Symmetry, Matrix4, Matrix4TMD
transpose() : Tensor, Matrix4Symmetry, Matrix4, Matrix4TMD, colvarmodule::rmatrix
transvec() : Matrix4
transvecinv() : Matrix4
tree : ProxySpanningTreeMsg
TREE_WIDTH : DataExchanger
TreeJoin : parm
trees : ProxyTree
triangular() : Tensor
tstep : IMDEnergies
tupleList : ComputeHomeTuples< T, S, P >
tupleParamType : TupleSignature
TuplePatchElem() : TuplePatchElem
tuplePatchList : ComputeHomeTuples< T, S, P >
TupleSignature() : TupleSignature
tupleType : TupleSignature
TURN : PDBData
TVECT : PDBData
twoAwayX : SimParameters
twoAwayY : SimParameters
twoAwayZ : SimParameters
TwoTargets() : AForcingDiheRestraint, ABoundDiheRestraint, AFixedDiheRestraint, ADiheRestraint
type : PDBData, ComputeMap, Compute, colvarvalue, colvar::cvc, colvar, ParseOptions::DataElement, IMDheader, GridforceGrid, ComputeMap::ComputeData
Type : colvarvalue
type_checking() : colvarvalue
type_desc : colvarvalue
type_notset : colvarvalue
type_quaternion : colvarvalue
type_scalar : colvarvalue
type_unitvector : colvarvalue
type_vector : colvarvalue
tz : wkf_timer

- u -

u : minpoint, ComputeMsmMgr
uelec : NL_Msm_t
uidata : ParseOptions::DataElement
uidef : ParseOptions::DataElement
UINT : ParseOptions::DataElement
uiptr : ParseOptions::DataElement
unchecked_insert() : IRSet
UNDEF : ParseOptions::DataElement
undef_op() : colvarvalue
ungridCalc() : OptPmeMgr, ComputePmeMgr
ungridCalc_subcompute() : OptPmeMgr
ungridCalc_subcompute_done() : OptPmeMgr
ungridForces() : ComputePme
ungridForces_compute() : OptPmeCompute
ungridForces_finalize() : OptPmeCompute
ungridForces_init() : OptPmeCompute
uniform() : Random
uniq() : SortableResizeArray< Elem >
UniqueSet() : UniqueSet< Elem >
UniqueSet<Elem> : UniqueSetRaw< Elem >
UniqueSetIter() : UniqueSetIter< T >
UniqueSetIter<Elem> : UniqueSetRaw< Elem >, EntryGlob< Elem >, UniqueSet< Elem >
UniqueSetRaw() : UniqueSetRaw< Elem >
UniqueSetRaw<Elem> : EntryGlob< Elem >, Entry< Elem >
UniqueSortedArray() : UniqueSortedArray< Elem >
UniqueSortedArray<Elem> : ResizeArrayRaw< Elem >
unit() : Vector, colvarmodule::rvector
unit_angstrom() : colvarproxy_namd, colvarproxy, colvarmodule
units : ParseOptions, ParseOptions::DataElement
UNKNOWN : PDBData
unpack() : ExclusionSignature, AtomSignature, TupleSignature, ProxySpanningTreeMsg, ProxyResultMsg, MovePatchesMsg, PatchMap, MigrateAtomsCombinedMsg, MigrateAtomsMsg, GridforceLiteGrid, GridforceFullSubGrid, GridforceFullMainGrid, GridforceFullBaseGrid, GridforceGrid, ComputeMap, ComputeGlobalResultsMsg, ComputeGlobalDataMsg, ComputeDPMEResultsMsg, ComputeDPMEDataMsg, ComputeConsForceMsg, DataStreamMsg
unpack_data() : MGridforceParamsList
unpack_grid() : GridforceGrid
unregisterAvgPositionPickup() : Patch
unregisterBornRadPickup() : Patch
unregisterDEdaSumDeposit() : Patch
unregisterDHdrPrefixPickup() : Patch
unregisterForceDeposit() : Patch
unregisterIDsCompAtomExt() : AtomMapper
unregisterIDsFullAtom() : AtomMapper
unregisterIntRadPickup() : Patch
unregisterLcpoTypePickup() : Patch
unregisterPatch() : PatchMap
unregisterPositionPickup() : Patch
unregisterProxy() : ProxyMgr, HomePatch
unregisterPsiSumDeposit() : Patch
unregisterVelocityPickup() : Patch
unscale() : Lattice
unsubscribe() : BroadcastMgr
update() : ComputeMsmMgr, colvarbias_meta, colvarbias_histogram, colvarbias_abf, colvarbias_harmonic, colvarbias, colvar
update_replicas_registry() : colvarbias_meta
update_status : colvarbias_meta
updateComputes() : ComputeMgr
updateComputes2() : ComputeMgr
updateComputes3() : ComputeMgr
updateComputesReady() : LdbCoordinator
UpdateCOMs() : ARestraintManager, ARestraint
updateLocalComputes() : ComputeMgr
updateLocalComputes2() : ComputeMgr
updateLocalComputes3() : ComputeMgr
updateLocalComputes4() : ComputeMgr
updateLocalComputes5() : ComputeMgr
UpdateLocalLBInfo() : NamdHybridLB
updateLower() : msm::Grid< T >, msm::GridFixed< T, N >
updateMolInfo() : ParallelIOMgr
updatetime : wkfmsgtimer
upper_boundaries : colvar_grid< T >
upper_boundary : colvar
upper_wall : colvar
upper_wall_k : colvar
upstreamNeighbors() : PatchMap
USE_ATOM : PDBAtom
use_grids : colvarbias_meta
USE_HETATM : PDBAtom
use_imd() : IMDOutput
useAntecedent : SimParameters
useAvgPositions : ComputeHomePatches
useCkLoop : SimParameters
useCompressedPsf : SimParameters
useConstantArea : SimParameters
useConstantRatio : SimParameters
useController() : NamdState
useDPME : SimParameters
useFlexibleCell : SimParameters
useGroupPressure : SimParameters
useManyToMany : SimParameters
useOptPME : SimParameters
usePairlists : SimParameters, Flags, nonbonded
usePluginIO : SimParameters
useSequencer() : HomePatch
useSettle : SimParameters

- v -

v : Patch, nonbonded, ComputeMsmMgr
v12 : colvar::distance_xy
v13 : colvar::distance_xy
v_fdiff : colvar
v_reported : colvar
v_vdwa : ComputeNonbondedUtil
v_vdwb : ComputeNonbondedUtil
valid : ComputeLCPO
value : colvar_grid< T >, colvar::cvc, colvarbias_meta::hill, colvar, ScriptParamMsg, TholeElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
value_input() : colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvar_grid< T >
value_output() : colvar_grid_gradient, colvar_grid_scalar, colvar_grid< T >
value_to_bin_scalar() : colvar_grid< T >
value_type : colvarvalue
values : ImproperValue, DihedralValue, crossterm_params, improper_params, dihedral_params
vdata : ParseOptions::DataElement
vdef : ParseOptions::DataElement
vdw_array : Parameters
vdw_pair_tree : Parameters
vdw_type : AtomCstInfo, atom_constants, OutputAtomRecord::shortVals
vdwa_table : ComputeNonbondedUtil
vdwb_table : ComputeNonbondedUtil
vdwEnergyIndex : ComputeNonbondedUtil, ExclElem
vdwEnergyIndex_s : ComputeNonbondedUtil
vdwEnergyIndex_s_Left : ComputeNonbondedUtil
vdwEnergyIndex_ti_1 : ComputeNonbondedUtil
vdwEnergyIndex_ti_2 : ComputeNonbondedUtil
vdwForceSwitching : SimParameters
vdwGeometricSigma : SimParameters
vdwscale14 : SimParameters
vdwType : CompAtom, ComputeGBISAtom
Vector() : Vector
VECTOR : ParseOptions::DataElement
vector1d() : colvarmodule::vector1d< T, length >
VectorValid : CollectVectorVarMsg
vel : colvarmodule::atom
velDcdFilename : SimParameters
velDcdFrequency : SimParameters
velem : C1Vector
velocities() : colvarmodule::atom_group
velocity : Output, colvar, FullAtom
velocityBox : Patch, ComputeNonbondedSelf, ComputeNonbondedPair
velocityBoxClosed() : Patch
velocityComputeList : Patch
velocityList : ProxyDataMsg
velocityNeeded() : Output
velocityPtrBegin : Patch
velocityPtrEnd : Patch
velocityRescaleFactor : ControllerBroadcasts
virial : MsmSerialForceMsg, ComputeMsmMgr, FmmSerialForceMsg, ExtForceMsg
virial_amd : Controller
virialIndex : TholeElem, ComputeNonbondedUtil, ExclElem, ImproperElem, DihedralElem, CrosstermElem, BondElem, AnisoElem, AngleElem
vlLen : ProxyDataMsg
VMAX : ComputeMsmMgr
volume() : Lattice
vptr : ParseOptions::DataElement
vr : colvar
VXX : ComputeMsmMgr
VXY : ComputeMsmMgr
VXZ : ComputeMsmMgr
VYY : ComputeMsmMgr
VYZ : ComputeMsmMgr
VZZ : ComputeMsmMgr

- w -

w : ComputeMsmMgr
W : colvarbias_meta::hill
waitForTag : BroadcastClient
waitingForSequenceNumber : ReductionSet
waitingThread : ReductionSet
waterVal : HydrogenGroupID
watmodel : SimParameters
WCA_rcut1 : ComputeNonbondedUtil
WCA_rcut2 : ComputeNonbondedUtil
WCA_rcut3 : ComputeNonbondedUtil
weight() : colvarbias_meta::hill
well_tempered : colvarbias_meta
white_space : colvarparse
width : colvar
widths : colvar_grid< T >, colvarbias_meta::hill
willRequire() : ReductionMgr
willSubmit() : ReductionMgr
window() : Matrix4
withinBrick() : Rebalancer
work : NamdDummyLB, OptPmePencil< T >, PmePencil< T >, WorkIndex
workArrays : nonbonded, ComputeNonbondedSelf, ComputeNonbondedPair, ComputeLCPO
WorkDistrib : WorkDistrib, PatchMap, Molecule, ComputeMap
workDistrib : Node, BOCgroup
WorkIndex() : WorkIndex
workStarted : ComputeNonbondedCUDA
wrap() : colvar_grid< T >, colvar::spin_angle, colvar::dihedral, colvar::distance_z, colvar::cvc, colvar
wrap_center : colvar::cvc
wrap_delta() : Lattice
wrap_nearest_delta() : Lattice
wrap_position() : GridforceGrid
wrap_string() : colvarmodule
wrapAll : SimParameters
wrapBlockIndex() : msm::Map
wrapBlockSend() : msm::Map
wrapBlockSendFold() : msm::Map
wrapCoor() : ParallelIOMgr
wrapCoorFinished() : CollectionMaster
wrapNearest : SimParameters
wrapWater : SimParameters
write() : PDB
write_1D_integral() : colvar_grid_gradient
write_acf() : colvar
write_multicol() : colvar_grid< T >
write_output_files() : colvarmodule, colvar
write_params() : colvar_grid< T >
write_pmf() : colvarbias_meta
write_raw() : colvar_grid< T >
write_replica_state_file() : colvarbias_meta
write_restart() : colvarmodule, colvar_grid_gradient, colvar_grid_scalar, colvar_grid_count, colvarbias_meta, colvarbias_harmonic, colvarbias, colvar
write_traj() : colvar
write_traj_label() : colvar
writeExtendedSystemData() : Controller
writeExtendedSystemLabels() : Controller
writeFepEnergyData() : Controller
writeTiEnergyData() : Controller

- x -

x : Vector, FloatVector, PmeParticle, CudaAtom, minpoint, ComputeNonbondedCUDA::patch_record, LCPOAtom, TuplePatchElem, PatchElem, vect, EwaldParticle, colvarmodule::rvector, colvar::cvc, colvar
x0 : NonbondedExclValue, BondValue
x_avg : TuplePatchElem
x_history : colvar
x_history_p : colvar
x_old : colvar::cvc, colvar
x_reported : colvar
x_start : LocalPmeInfo, PmeTransMsg
xBlocks : PmeGrid, PmeFFTInfo, OptPmePencilInitMsgData, PmePencilInitMsgData
Xcap : parm
xcoor() : PDBAtom
xExt : ComputeNonbondedCUDA::patch_record, TuplePatchElem
xlen : PatchGridElem, OptPmeGridMsg
xloopcnt : MsmProfiler
xm : NodePmeMgr, PmePencilInitMsgData
xmax : PencilElement
xmin : PencilElement
xPencil : OptPmePencilInitMsgData, PmePencilInitMsgData
xr : colvar
xstart : PatchGridElem, OptPmeGridMsg
xstFile : Controller
xstFilename : SimParameters
xstFrequency : SimParameters
xx : colvarmodule::rmatrix, Tensor
xy : colvarmodule::rmatrix, Tensor
xz : colvarmodule::rmatrix, Tensor

- y -

y : Vector, FloatVector, PmeParticle, CudaAtom, LCPOAtom, vect, EwaldParticle, colvarmodule::rvector
y_start : PmeUntransMsg
y_start_after_transpose : LocalPmeInfo
yBlocks : PmeGrid, PmeFFTInfo, OptPmePencilInitMsgData, PmePencilInitMsgData
Ycap : parm
ycoor() : PDBAtom
ylen : PatchGridElem, OptPmeGridMsg
ym : NodePmeMgr, PmePencilInitMsgData
ymax : PencilElement
ymin : PencilElement
yPencil : OptPmePencilInitMsgData, PmePencilInitMsgData
ystart : PatchGridElem, OptPmeGridMsg
yx : colvarmodule::rmatrix, Tensor
yy : colvarmodule::rmatrix, Tensor
yz : colvarmodule::rmatrix, Tensor

- z -

z : Vector, FloatVector, PmeParticle, CudaAtom, LCPOAtom, vect, EwaldParticle, colvarmodule::rvector
zBlocks : PmeGrid, PmeFFTInfo, OptPmePencilInitMsgData, PmePencilInitMsgData
Zcap : parm
zcoor() : PDBAtom
zero_derivs : GridforceFullBaseGrid::GridIndices
ZeroAccumulator() : ALambdaManager, ALambdaControl
zeroMomentum : SimParameters
zeroMomentumAlt : SimParameters
zlen : PatchGridElem, OptPmeGridMsg
zline_storage : OptPmeCompute
zlist : PmeGridMsg
zlistlen : PmeGridMsg
zm : NodePmeMgr, PmePencilInitMsgData
zmax : PencilElement
zmin : PencilElement
zPencil : OptPmePencilInitMsgData, PmePencilInitMsgData
zstart : PatchGridElem, OptPmeGridMsg
zVector() : zVector
zx : colvarmodule::rmatrix, Tensor
zy : colvarmodule::rmatrix, Tensor
zz : colvarmodule::rmatrix, Tensor

- ~ -

~AGroup() : AGroup
~ALambdaManager() : ALambdaManager
~alpha_angles() : colvar::alpha_angles
~angle() : colvar::angle
~AngleElem() : AngleElem
~AnisoElem() : AnisoElem
~ARestraint() : ARestraint
~ARestraintManager() : ARestraintManager
~Array() : msm::Array< T >, Array< Elem, Size >
~atom() : colvarmodule::atom
~atom_group() : colvarmodule::atom_group
~AtomMap() : AtomMap
~AtomMapper() : AtomMapper
~AtomSigInfo() : AtomSigInfo
~AtomSignature() : AtomSignature
~BOID() : BOID
~BondElem() : BondElem
~BroadcastClient() : BroadcastClient
~BroadcastClientElem() : BroadcastClientElem
~BroadcastMgr() : BroadcastMgr
~BroadcastMsg() : BroadcastMsg
~CollectionMaster() : CollectionMaster
~CollectionMgr() : CollectionMgr
~colvar() : colvar
~colvar_grid() : colvar_grid< T >
~colvar_grid_count() : colvar_grid_count
~colvar_grid_gradient() : colvar_grid_gradient
~colvar_grid_scalar() : colvar_grid_scalar
~colvarbias() : colvarbias
~colvarbias_abf() : colvarbias_abf
~colvarbias_harmonic() : colvarbias_harmonic
~colvarbias_histogram() : colvarbias_histogram
~colvarbias_meta() : colvarbias_meta
~colvarmodule() : colvarmodule
~colvarproxy() : colvarproxy
~colvarproxy_namd() : colvarproxy_namd
~Communicate() : Communicate
~Compute() : Compute
~ComputeConsForce() : ComputeConsForce
~ComputeConsForceMsg() : ComputeConsForceMsg
~ComputeConsTorque() : ComputeConsTorque
~ComputeCylindricalBC() : ComputeCylindricalBC
~ComputeDPMEDataMsg() : ComputeDPMEDataMsg
~ComputeDPMEResultsMsg() : ComputeDPMEResultsMsg
~ComputeEField() : ComputeEField
~ComputeEwald() : ComputeEwald
~ComputeExt() : ComputeExt
~ComputeExtMgr() : ComputeExtMgr
~ComputeFmmSerial() : ComputeFmmSerial
~ComputeFmmSerialMgr() : ComputeFmmSerialMgr
~ComputeFullDirect() : ComputeFullDirect
~ComputeGBISser() : ComputeGBISser
~ComputeGBISserMgr() : ComputeGBISserMgr
~ComputeGlobal() : ComputeGlobal
~ComputeGlobalDataMsg() : ComputeGlobalDataMsg
~ComputeGlobalResultsMsg() : ComputeGlobalResultsMsg
~ComputeGridForce() : ComputeGridForce
~ComputeHomePatch() : ComputeHomePatch
~ComputeHomePatches() : ComputeHomePatches
~ComputeHomeTuples() : ComputeHomeTuples< T, S, P >
~ComputeLCPO() : ComputeLCPO
~ComputeMap() : ComputeMap
~ComputeMgr() : ComputeMgr
~ComputeMoa() : ComputeMoa
~ComputeMsm() : ComputeMsm
~ComputeMsmMgr() : ComputeMsmMgr
~ComputeMsmSerial() : ComputeMsmSerial
~ComputeMsmSerialMgr() : ComputeMsmSerialMgr
~ComputeNonbondedCUDA() : ComputeNonbondedCUDA
~ComputeNonbondedPair() : ComputeNonbondedPair
~ComputeNonbondedSelf() : ComputeNonbondedSelf
~ComputeNonbondedUtil() : ComputeNonbondedUtil
~ComputePatch() : ComputePatch
~ComputePatchPair() : ComputePatchPair
~ComputePme() : ComputePme
~ComputePmeMgr() : ComputePmeMgr
~ComputeRestraints() : ComputeRestraints
~ComputeSelfTuples() : ComputeSelfTuples< T, S, P >
~ComputeSphericalBC() : ComputeSphericalBC
~ComputeStir() : ComputeStir
~ComputeTclBC() : ComputeTclBC
~ConfigList() : ConfigList
~ConfigListNode() : ConfigList::ConfigListNode
~Controller() : Controller
~coordnum() : colvar::coordnum
~crossterm_params() : crossterm_params
~CrosstermElem() : CrosstermElem
~cvc() : colvar::cvc
~DataElement() : ParseOptions::DataElement
~DataExchanger() : DataExchanger
~datastream() : datastream
~dihedPC() : colvar::dihedPC
~dihedral() : colvar::dihedral
~DihedralElem() : DihedralElem
~distance() : colvar::distance
~distance_dir() : colvar::distance_dir
~distance_inv() : colvar::distance_inv
~distance_vec() : colvar::distance_vec
~distance_xy() : colvar::distance_xy
~distance_z() : colvar::distance_z
~eigenvector() : colvar::eigenvector
~Entry() : Entry< Elem >
~EntryGlob() : EntryGlob< Elem >
~ExclElem() : ExclElem
~ExclSigInfo() : ExclSigInfo
~ExclusionCheck() : ExclusionCheck
~ExclusionSignature() : ExclusionSignature
~floatcomplex() : floatcomplex
~GlobalMaster() : GlobalMaster
~GlobalMasterEasy() : GlobalMasterEasy
~GlobalMasterFreeEnergy() : GlobalMasterFreeEnergy
~GlobalMasterIMD() : GlobalMasterIMD
~GlobalMasterMisc() : GlobalMasterMisc
~GlobalMasterServer() : GlobalMasterServer
~GlobalMasterSMD() : GlobalMasterSMD
~GlobalMasterSymmetry() : GlobalMasterSymmetry
~GlobalMasterTcl() : GlobalMasterTcl
~GlobalMasterTMD() : GlobalMasterTMD
~GridforceFullBaseGrid() : GridforceFullBaseGrid
~GridforceFullMainGrid() : GridforceFullMainGrid
~GridforceLiteGrid() : GridforceLiteGrid
~gyration() : colvar::gyration
~h_bond() : colvar::h_bond
~HashPool() : HashPool< T >
~hill() : colvarbias_meta::hill
~HomePatch() : HomePatch
~HomePatchElem() : HomePatchElem
~HydrogenGroupID() : HydrogenGroupID
~IMDOutput() : IMDOutput
~ImproperElem() : ImproperElem
~inertia() : colvar::inertia
~inertia_z() : colvar::inertia_z
~infostream() : infostream
~IRSet() : IRSet
~LCPONeighborList() : LCPONeighborList
~LdbCoordinator() : LdbCoordinator
~LJTable() : LJTable
~MathArray() : MathArray< Elem, Size >
~matrix2d() : colvarmodule::matrix2d< T, outer_length, inner_length >
~Matrix4() : Matrix4
~maxHeap() : maxHeap
~MGridforceParamsList() : MGridforceParamsList
~MigrateAtomsCombinedMsg() : MigrateAtomsCombinedMsg
~minHeap() : minHeap
~MIStream() : MIStream
~Molecule() : Molecule
~MOStream() : MOStream
~MovePatch() : MovePatch
~NamdState() : NamdState
~Node() : Node
~NodePmeMgr() : NodePmeMgr
~NodeProxyMgr() : NodeProxyMgr
~ObjectArena() : ObjectArena< Type >
~OptPmeCompute() : OptPmeCompute
~OptPmeMgr() : OptPmeMgr
~OptPmePencil() : OptPmePencil< T >
~OptPmeRealSpace() : OptPmeRealSpace
~orientation() : colvar::orientation
~orientation_angle() : colvar::orientation_angle
~Output() : Output
~OwnerBox() : OwnerBox< Owner, Data >
~Pairlists() : Pairlists
~ParallelIOMgr() : ParallelIOMgr
~Parameters() : Parameters
~parm() : parm
~ParseOptions() : ParseOptions
~Patch() : Patch
~PatchElem() : PatchElem
~PatchMap() : PatchMap
~PatchMgr() : PatchMgr
~PDB() : PDB
~PDBAtom() : PDBAtom
~PDBAtomRecord() : PDBAtomRecord
~PDBData() : PDBData
~PDBHetatm() : PDBHetatm
~PDBUnknown() : PDBUnknown
~PluginIOMgr() : PluginIOMgr
~PmeKSpace() : PmeKSpace
~PmePencil() : PmePencil< T >
~PmeRealSpace() : PmeRealSpace
~PmeXPencil() : PmeXPencil
~PmeZPencil() : PmeZPencil
~PressureProfileReduction() : PressureProfileReduction
~ProxyMgr() : ProxyMgr
~ProxyPatch() : ProxyPatch
~ProxyTree() : ProxyTree
~proxyTreeNode() : proxyTreeNode
~read_block() : colvarparse::read_block
~Rebalancer() : Rebalancer
~RecBisection() : RecBisection
~ReductionMgr() : ReductionMgr
~ReductionSet() : ReductionSet
~ReductionSetData() : ReductionSetData
~RefineTorusLB() : RefineTorusLB
~RequireReduction() : RequireReduction
~ResidueLookupElem() : ResidueLookupElem
~ResizeArray() : ResizeArray< Elem >
~ResizeArrayIter() : ResizeArrayIter< T >
~ResizeArrayPrimIter() : ResizeArrayPrimIter< T >
~rmatrix() : colvarmodule::rmatrix
~rmsd() : colvar::rmsd
~rotation() : colvarmodule::rotation
~ScriptTcl() : ScriptTcl
~selfcoordnum() : colvar::selfcoordnum
~Sequencer() : Sequencer
~SimParameters() : SimParameters
~SimpleBroadcastObject() : SimpleBroadcastObject< T >
~SortableResizeArray() : SortableResizeArray< Elem >
~spin_angle() : colvar::spin_angle
~StringList() : StringList
~SubmitReduction() : SubmitReduction
~Sync() : Sync
~TaggedMsg() : TaggedMsg
~Tensor() : Tensor
~TholeElem() : TholeElem
~tilt() : colvar::tilt
~TorusLB() : TorusLB
~TuplePatchElem() : TuplePatchElem
~TupleSignature() : TupleSignature
~UniqueSet() : UniqueSet< Elem >
~UniqueSetIter() : UniqueSetIter< T >
~UniqueSetRaw() : UniqueSetRaw< Elem >
~vector1d() : colvarmodule::vector1d< T, length >
~WorkDistrib() : WorkDistrib

Generated on Wed May 22 04:07:20 2013 for NAMD by

1.3.9.1