NAMD
Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
SimParameters Class Reference

#include <SimParameters.h>

Public Member Functions

BigReal getCurrentLambda (const int)
 
BigReal getCurrentLambda2 (const int)
 
int setupIDWS ()
 
BigReal getLambdaDelta (void)
 
BigReal getElecLambda (const BigReal)
 
BigReal getVdwLambda (const BigReal)
 
BigReal getRepLambda (const BigReal)
 
BigReal getBondLambda (const BigReal)
 
 SimParameters ()
 
 SimParameters (ConfigList *c, char *&cwd)
 
 ~SimParameters ()
 
void initialize_config_data (ConfigList *, char *&cwd)
 
void send_SimParameters (MOStream *)
 
void receive_SimParameters (MIStream *)
 
void scriptSet (const char *, const char *)
 
void close_dcdfile ()
 
void close_veldcdfile ()
 
int isSendSpanningTreeOn ()
 
int isSendSpanningTreeUnset ()
 
int isRecvSpanningTreeOn ()
 
int isRecvSpanningTreeUnset ()
 
char * getfromparseopts (const char *name, char *outbuf)
 
int istrueinparseopts (const char *name)
 
int issetinparseopts (const char *name)
 
void readExtendedSystem (const char *filename, Lattice *latptr=0)
 

Static Public Member Functions

static void nonbonded_select ()
 
static void pme_select ()
 

Public Attributes

Bool lonepairs
 
int watmodel
 
Bool LJcorrection
 
BigReal dt
 
int N
 
int stepsPerCycle
 
zVector cellBasisVector1
 
zVector cellBasisVector2
 
zVector cellBasisVector3
 
zVector cellOrigin
 
Lattice lattice
 
int nonbondedFrequency
 
int fullElectFrequency
 
BigReal fmaTheta
 
int ldBalancer
 
int ldbStrategy
 
int ldbPeriod
 
int firstLdbStep
 
int lastLdbStep
 
int hybridGroupSize
 
BigReal ldbBackgroundScaling
 
BigReal ldbPMEBackgroundScaling
 
BigReal ldbHomeBackgroundScaling
 
BigReal ldbRelativeGrainsize
 
int traceStartStep
 
int numTraceSteps
 
Bool outputMaps
 
Bool simulateInitialMapping
 
int simulatedPEs
 
int simulatedNodeSize
 
Bool disableTopology
 
Bool verboseTopology
 
Bool benchTimestep
 
int useCkLoop
 
int twoAwayX
 
int twoAwayY
 
int twoAwayZ
 
int maxPatches
 
Bool ldbUnloadPME
 
Bool ldbUnloadZero
 
Bool ldbUnloadOne
 
Bool ldbUnloadOutputPEs
 
Bool noPatchesOnZero
 
Bool noPatchesOnOutputPEs
 
Bool noPatchesOnOne
 
BigReal initialTemp
 
Bool comMove
 
Bool zeroMomentum
 
Bool zeroMomentumAlt
 
Bool wrapWater
 
Bool wrapAll
 
Bool wrapNearest
 
BigReal dielectric
 
ExclusionSettings exclude
 
BigReal scale14
 
BigReal nonbondedScaling
 
int dcdFrequency
 
int dcdUnitCell
 
int velDcdFrequency
 
int forceDcdFrequency
 
int xstFrequency
 
char auxFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char dcdFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char velDcdFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char forceDcdFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char xstFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char outputFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char restartFilename [NAMD_FILENAME_BUFFER_SIZE]
 
int restartFrequency
 
Bool restartSave
 
Bool restartSaveDcd
 
Bool binaryRestart
 
Bool binaryOutput
 
BigReal cutoff
 
BigReal margin
 
BigReal patchDimension
 
BigReal limitDist
 
Bool switchingActive
 
Bool vdwForceSwitching
 
BigReal switchingDist
 
Bool martiniSwitching
 
Bool martiniDielAllow
 
BigReal pairlistDist
 
int pairlistMinProcs
 
int usePairlists
 
int pairlistsPerCycle
 
BigReal pairlistShrink
 
BigReal pairlistGrow
 
BigReal pairlistTrigger
 
int outputPairlists
 
Bool constraintsOn
 
int constraintExp
 
Bool gridforceOn
 
Bool gridforceVolts
 
zVector gridforceScale
 
Bool gridforceContA1
 
Bool gridforceContA2
 
Bool gridforceContA3
 
zVector gridforceVOffset
 
Bool gridforceLite
 
Bool gridforcechecksize
 
Bool mgridforceOn
 
MGridforceParamsList mgridforcelist
 
Bool selectConstraintsOn
 
Bool constrXOn
 
Bool constrYOn
 
Bool constrZOn
 
Bool sphericalConstraintsOn
 
zVector sphericalConstrCenter
 
BigReal constraintScaling
 
Bool paraTypeXplorOn
 
Bool paraTypeCharmmOn
 
Bool goGroPair
 
Bool goForcesOn
 
char goParameters [NAMD_FILENAME_BUFFER_SIZE]
 
char goCoordinates [NAMD_FILENAME_BUFFER_SIZE]
 
GoChoices goMethod
 
Bool movingConstraintsOn
 
zVector movingConsVel
 
Bool rotConstraintsOn
 
zVector rotConsAxis
 
zVector rotConsPivot
 
BigReal rotConsVel
 
Bool movDragOn
 
char movDragFile [NAMD_FILENAME_BUFFER_SIZE]
 
BigReal movDragGlobVel
 
char movDragVelFile [NAMD_FILENAME_BUFFER_SIZE]
 
Bool rotDragOn
 
char rotDragFile [NAMD_FILENAME_BUFFER_SIZE]
 
char rotDragAxisFile [NAMD_FILENAME_BUFFER_SIZE]
 
char rotDragPivotFile [NAMD_FILENAME_BUFFER_SIZE]
 
BigReal rotDragGlobVel
 
char rotDragVelFile [NAMD_FILENAME_BUFFER_SIZE]
 
Bool consTorqueOn
 
char consTorqueFile [NAMD_FILENAME_BUFFER_SIZE]
 
char consTorqueAxisFile [NAMD_FILENAME_BUFFER_SIZE]
 
char consTorquePivotFile [NAMD_FILENAME_BUFFER_SIZE]
 
BigReal consTorqueGlobVal
 
char consTorqueValFile [NAMD_FILENAME_BUFFER_SIZE]
 
Bool SMDOn
 
BigReal SMDVel
 
zVector SMDDir
 
BigReal SMDk
 
BigReal SMDk2
 
char SMDFile [NAMD_FILENAME_BUFFER_SIZE]
 
int SMDOutputFreq
 
Bool tabulatedEnergies
 
int tableNumTypes
 
char tabulatedEnergiesFile [NAMD_FILENAME_BUFFER_SIZE]
 
char tableInterpType [128]
 
Real tableSpacing
 
BigReal tableMaxDist
 
Bool TMDOn
 
Bool TMDDiffRMSD
 
BigReal TMDk
 
char TMDFile [NAMD_FILENAME_BUFFER_SIZE]
 
char TMDFile2 [NAMD_FILENAME_BUFFER_SIZE]
 
int TMDOutputFreq
 
int TMDFirstStep
 
int TMDLastStep
 
BigReal TMDInitialRMSD
 
BigReal TMDFinalRMSD
 
Bool symmetryOn
 
Bool symmetryScaleForces
 
BigReal symmetryk
 
char symmetrykfile [NAMD_FILENAME_BUFFER_SIZE]
 
char symmetryFile [NAMD_FILENAME_BUFFER_SIZE]
 
char symmetryMatrixFile [NAMD_FILENAME_BUFFER_SIZE]
 
int symmetryFirstStep
 
int symmetryLastStep
 
int symmetryFirstFullStep
 
int symmetryLastFullStep
 
Bool alchOnAtStartup
 
Bool alchFepOnAtStartup
 
Bool alchThermIntOnAtStartup
 
Bool alchOn
 
Bool alchFepOn
 
Bool singleTopology
 
Bool sdScaling
 
Bool alchThermIntOn
 
Bool alchWCAOn
 
int alchMethod
 
BigReal alchLambda
 
BigReal alchLambda2
 
BigReal alchLambdaIDWS
 
int alchIDWSFreq
 
int alchLambdaFreq
 
BigReal alchTemp
 
int alchOutFreq
 
Bool alchEnsembleAvg
 
char alchOutFile [NAMD_FILENAME_BUFFER_SIZE]
 
int alchEquilSteps
 
BigReal alchVdwShiftCoeff
 
BigReal alchElecLambdaStart
 
BigReal alchVdwLambdaEnd
 
BigReal alchRepLambdaEnd
 
BigReal alchBondLambdaEnd
 
Bool alchDecouple
 
Bool alchBondDecouple
 
Bool lesOn
 
int lesFactor
 
Bool lesReduceTemp
 
Bool lesReduceMass
 
Bool soluteScalingOn
 
BigReal soluteScalingFactor
 
BigReal soluteScalingFactorCharge
 
BigReal soluteScalingFactorVdw
 
Bool soluteScalingAll
 
Bool extForcesOn
 
char extForcesCommand [NAMD_FILENAME_BUFFER_SIZE]
 
char extCoordFilename [NAMD_FILENAME_BUFFER_SIZE]
 
char extForceFilename [NAMD_FILENAME_BUFFER_SIZE]
 
Bool qmForcesOn
 
char qmParamPDB [NAMD_FILENAME_BUFFER_SIZE]
 
Bool qmParamPDBDefined
 
Bool qmChrgFromPSF
 
char qmExecPath [NAMD_FILENAME_BUFFER_SIZE]
 
char qmSoftware [128]
 
char qmChrgModeS [16]
 
int qmChrgMode
 
char qmColumn [16]
 
char qmBaseDir [NAMD_FILENAME_BUFFER_SIZE]
 
char qmSecProc [NAMD_FILENAME_BUFFER_SIZE]
 
Bool qmSecProcOn
 
char qmPrepProc [NAMD_FILENAME_BUFFER_SIZE]
 
Bool qmPrepProcOn
 
int qmFormat
 
Bool qmReplaceAll
 
Bool qmMOPACAddConfigChrg
 
Bool qmBondOn
 
char qmBondColumn [16]
 
Bool qmBondDist
 
int qmBondValType
 
char qmBondValueTypeS [16]
 
char qmBondSchemeS [16]
 
int qmBondScheme
 
Bool qmPCSwitchOn
 
char qmPCSwitchTypeS [16]
 
int qmPCSwitchType
 
char qmPCSchemeS [16]
 
int qmPCScheme
 
int qmSimsPerNode
 
Bool qmVDW
 
Bool qmNoPC
 
Bool qmElecEmbed
 
int qmPCSelFreq
 
Bool qmCustomPCSel
 
Bool qmLSSOn
 
int qmLSSFreq
 
char qmLSSResname [5]
 
char qmLSSModeS [16]
 
int qmLSSMode
 
Bool qmCSMD
 
char qmCSMDFile [NAMD_FILENAME_BUFFER_SIZE]
 
int qmEnergyOutFreq
 
int qmOutFreq
 
int qmPosOutFreq
 
Bool printBadContacts
 
Bool GBISOn
 
BigReal fsMax
 
Bool GBISserOn
 
BigReal solvent_dielectric
 
BigReal coulomb_radius_offset
 
BigReal kappa
 
BigReal ion_concentration
 
BigReal gbis_delta
 
BigReal gbis_beta
 
BigReal gbis_gamma
 
BigReal alpha_cutoff
 
BigReal alpha_max
 
Bool LCPOOn
 
BigReal surface_tension
 
Bool drudeOn
 
Bool drudeHardWallOn
 
BigReal drudeTemp
 
BigReal drudeDamping
 
BigReal drudeBondLen
 
BigReal drudeBondConst
 
BigReal drudeNbtholeCut
 
Bool pairInteractionOn
 
int pairInteractionGroup1
 
int pairInteractionGroup2
 
Bool pairInteractionSelf
 
Bool cosAngles
 
Bool globalForcesOn
 
Bool tclForcesOn
 
Bool tclIsThreaded
 
Bool tclBCOn
 
char * tclBCScript
 
char tclBCArgs [NAMD_FILENAME_BUFFER_SIZE]
 
Bool freeEnergyOn
 
Bool miscForcesOn
 
Bool colvarsOn
 
Bool fixedAtomsOn
 
Bool fixedAtomsForces
 
Bool fixedAtomsForceOutput
 
Bool langevinOnAtStartup
 
Bool langevinOn
 
BigReal langevinTemp
 
BigReal langevinDamping
 
Bool langevinHydrogen
 
Bool langevin_useBAOAB
 
Bool loweAndersenOn
 
BigReal loweAndersenTemp
 
BigReal loweAndersenRate
 
BigReal loweAndersenCutoff
 
Bool globalOn
 
Bool dihedralOn
 
Bool COLDOn
 
BigReal COLDRate
 
BigReal COLDTemp
 
Bool tCoupleOn
 
BigReal tCoupleTemp
 
Bool stochRescaleOn
 
BigReal stochRescaleTemp
 
BigReal stochRescalePeriod
 
int stochRescaleFreq
 
Bool stochRescaleHeat
 
int rescaleFreq
 
BigReal rescaleTemp
 
Bool accelMDOn
 
Bool accelMDdihe
 
Bool accelMDdual
 
Bool accelMDDebugOn
 
BigReal accelMDFirstStep
 
BigReal accelMDLastStep
 
int accelMDOutFreq
 
BigReal accelMDE
 
BigReal accelMDalpha
 
BigReal accelMDTE
 
BigReal accelMDTalpha
 
Bool accelMDG
 
int accelMDGiE
 
int accelMDGcMDSteps
 
int accelMDGEquiSteps
 
int accelMDGcMDPrepSteps
 
int accelMDGEquiPrepSteps
 
int accelMDGStatWindow
 
BigReal accelMDGSigma0P
 
BigReal accelMDGSigma0D
 
Bool accelMDGRestart
 
char accelMDGRestartFile [NAMD_FILENAME_BUFFER_SIZE]
 
Bool accelMDGresetVaftercmd
 
Bool adaptTempOn
 
Bool adaptTempDebug
 
int adaptTempFirstStep
 
int adaptTempLastStep
 
int adaptTempOutFreq
 
int adaptTempFreq
 
BigReal adaptTempTmin
 
BigReal adaptTempTmax
 
BigReal adaptTempAutoDt
 
int adaptTempBins
 
BigReal adaptTempDt
 
BigReal adaptTempCgamma
 
Bool adaptTempLangevin
 
Bool adaptTempRescale
 
char adaptTempInFile [NAMD_FILENAME_BUFFER_SIZE]
 
char adaptTempRestartFile [NAMD_FILENAME_BUFFER_SIZE]
 
int adaptTempRestartFreq
 
Bool adaptTempRandom
 
int reassignFreq
 
BigReal reassignTemp
 
BigReal reassignIncr
 
BigReal reassignHold
 
Bool useGroupPressure
 
Bool excludeFromPressure
 
Bool useFlexibleCell
 
Bool useConstantArea
 
Bool useConstantRatio
 
Bool fixCellDims
 
Bool fixCellDimX
 
Bool fixCellDimY
 
Bool fixCellDimZ
 
Bool berendsenPressureOn
 
BigReal berendsenPressureTarget
 
BigReal berendsenPressureCompressibility
 
BigReal berendsenPressureRelaxationTime
 
int berendsenPressureFreq
 
Bool langevinPistonOn
 
Bool langevinPistonBarrier
 
BigReal langevinPistonTarget
 
BigReal langevinPistonPeriod
 
BigReal langevinPistonDecay
 
BigReal langevinPistonTemp
 
Bool multigratorOn
 
BigReal multigratorPressureTarget
 
BigReal multigratorPressureRelaxationTime
 
int multigratorPressureFreq
 
BigReal multigratorTemperatureTarget
 
BigReal multigratorTemperatureRelaxationTime
 
int multigratorTemperatureFreq
 
int multigratorNoseHooverChainLength
 
BigReal surfaceTensionTarget
 
Bool pressureProfileOn
 
int pressureProfileSlabs
 
int pressureProfileFreq
 
int pressureProfileAtomTypes
 
Bool pressureProfileEwaldOn
 
int pressureProfileEwaldX
 
int pressureProfileEwaldY
 
int pressureProfileEwaldZ
 
zVector strainRate
 
zVector strainRate2
 
unsigned int randomSeed
 
Bool FMAOn
 
int FMALevels
 
int FMAMp
 
Bool FMAFFTOn
 
int FMAFFTBlock
 
Bool fullDirectOn
 
Bool MSMOn
 
int MSMQuality
 
int MSMApprox
 
int MSMSplit
 
int MSMLevels
 
int MSMBlockSizeX
 
int MSMBlockSizeY
 
int MSMBlockSizeZ
 
BigReal MSMGridSpacing
 
BigReal MSMPadding
 
BigReal MSMxmin
 
BigReal MSMxmax
 
BigReal MSMymin
 
BigReal MSMymax
 
BigReal MSMzmin
 
BigReal MSMzmax
 
Bool MsmSerialOn
 
Bool FMMOn
 
int FMMLevels
 
BigReal FMMPadding
 
Bool PMEOn
 
BigReal PMETolerance
 
BigReal PMEEwaldCoefficient
 
int PMEInterpOrder
 
int PMEGridSizeX
 
int PMEGridSizeY
 
int PMEGridSizeZ
 
BigReal PMEGridSpacing
 
int PMEProcessors
 
int PMEMinSlices
 
int PMEMinPoints
 
Bool PMEBarrier
 
int PMEPencils
 
int PMEPencilsX
 
int PMEPencilsY
 
int PMEPencilsZ
 
int PMEPencilsYLayout
 
int PMEPencilsXLayout
 
int PMESendOrder
 
Bool PMEOffload
 
Bool useDPME
 
Bool usePMECUDA
 
Bool useCUDA2
 
int bondedCUDA
 
Bool useCUDAdisable
 
Bool FFTWEstimate
 
Bool FFTWPatient
 
Bool FFTWUseWisdom
 
char FFTWWisdomFile [NAMD_FILENAME_BUFFER_SIZE]
 
char * FFTWWisdomString
 
Bool minimizeCGOn
 
Bool minVerbose
 
BigReal minTinyStep
 
BigReal minBabyStep
 
BigReal minLineGoal
 
Bool minimizeOn
 
BigReal maximumMove
 
Bool sphericalBCOn
 
zVector sphericalCenter
 
BigReal sphericalBCk1
 
BigReal sphericalBCk2
 
BigReal sphericalBCr1
 
BigReal sphericalBCr2
 
int sphericalBCexp1
 
int sphericalBCexp2
 
Bool cylindricalBCOn
 
zVector cylindricalCenter
 
char cylindricalBCAxis
 
BigReal cylindricalBCr1
 
BigReal cylindricalBCr2
 
BigReal cylindricalBCl1
 
BigReal cylindricalBCl2
 
int cylindricalBCexp1
 
int cylindricalBCexp2
 
BigReal cylindricalBCk1
 
BigReal cylindricalBCk2
 
Bool eFieldOn
 
Bool eFieldNormalized
 
zVector eField
 
BigReal eFieldFreq
 
BigReal eFieldPhase
 
Bool stirOn
 
char stirFilename [NAMD_FILENAME_BUFFER_SIZE]
 
BigReal stirStartingTheta
 
BigReal stirVel
 
BigReal stirK
 
zVector stirAxis
 
zVector stirPivot
 
Bool extraBondsOn
 
Bool extraBondsCosAngles
 
Bool extraBondsCosAnglesSetByUser
 
Bool consForceOn
 
char consForceFile [NAMD_FILENAME_BUFFER_SIZE]
 
BigReal consForceScaling
 
int outputEnergies
 
int outputEnergiesPrecision
 
int outputMomenta
 
int outputTiming
 
int outputCudaTiming
 
int outputPressure
 
Bool mergeCrossterms
 
int firstTimestep
 
MTSChoices MTSAlgorithm
 
int longSplitting
 
Bool ignoreMass
 
int splitPatch
 
BigReal hgroupCutoff
 
int mollyOn
 
BigReal mollyTol
 
int mollyIter
 
int rigidBonds
 
BigReal rigidTol
 
int rigidIter
 
int rigidDie
 
Bool useSettle
 
Bool testOn
 
Bool commOnly
 
Bool statsOn
 
int totalAtoms
 
int maxSelfPart
 
int maxPairPart
 
int numAtomsSelf
 
int numAtomsSelf2
 
int numAtomsPair
 
int numAtomsPair2
 
int minAtomsPerPatch
 
int emptyPatchLoad
 
int maxExclusionFlags
 
Bool outputPatchDetails
 
Bool staticAtomAssignment
 
Bool replicaUniformPatchGrids
 
Bool HydrogenBonds
 
Bool useAntecedent
 
int aaAngleExp
 
int haAngleExp
 
int distAttExp
 
int distRepExp
 
BigReal dhaCutoffAngle
 
BigReal dhaOnAngle
 
BigReal dhaOffAngle
 
BigReal daCutoffDist
 
BigReal daOnDist
 
BigReal daOffDist
 
int IMDon
 
int IMDport
 
int IMDfreq
 
int IMDwait
 
int IMDignore
 
int IMDignoreForces
 
Bool amberOn
 
Bool oldParmReader
 
Bool readExclusions
 
BigReal vdwscale14
 
Bool gromacsOn
 
Bool vdwGeometricSigma
 
BigReal scriptArg1
 
BigReal scriptArg2
 
BigReal scriptArg3
 
BigReal scriptArg4
 
BigReal scriptArg5
 
int scriptIntArg1
 
int scriptIntArg2
 
char scriptStringArg1 [128]
 
char scriptStringArg2 [128]
 
Bool useCompressedPsf
 
Bool genCompressedPsf
 
Bool usePluginIO
 
Bool mallocTest
 
Bool printExclusions
 
int proxySendSpanningTree
 
int proxyRecvSpanningTree
 
int proxyTreeBranchFactor
 
int numinputprocs
 
char * binAtomFile
 
char * binCoorFile
 
char * binVelFile
 
char * binRefFile
 
int numoutputprocs
 
int numoutputwrts
 
char computeMapFilename [NAMD_FILENAME_BUFFER_SIZE]
 
Bool storeComputeMap
 
Bool loadComputeMap
 
int mic_hostSplit
 
int mic_numParts_self_p1
 
int mic_numParts_pair_p1
 
int mic_numParts_pair_p2
 
int mic_unloadMICPEs
 
int mic_deviceThreshold
 
int mic_singleKernel
 
Bool useAVXTiles
 

Detailed Description

Definition at line 100 of file SimParameters.h.

Constructor & Destructor Documentation

SimParameters::SimParameters ( )
inline

Definition at line 1060 of file SimParameters.h.

1060 : mgridforcelist(), parseopts(0) {};
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:277
SimParameters::SimParameters ( ConfigList *  c,
char *&  cwd 
)
inline

Definition at line 1061 of file SimParameters.h.

References initialize_config_data().

1061  : mgridforcelist(), parseopts(0) {
1062  initialize_config_data(c,cwd);
1063  };
SimParameters::initialize_config_data
void initialize_config_data(ConfigList *, char *&cwd)
Definition: SimParameters.C:132
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:277
SimParameters::~SimParameters ( )
inline

Definition at line 1064 of file SimParameters.h.

1064 {};

Member Function Documentation

void SimParameters::close_dcdfile ( )

Definition at line 655 of file Output.C.

References END_OF_RUN, Node::Object(), and Node::output.

655  {
656 
657  Output *output = Node::Object()->output;
658  if ( ! output ) return;
659 
660  output->output_dcdfile(END_OF_RUN, 0, 0, 0);
661 
662 }
Node::Object
static Node * Object()
Definition: Node.h:86
Node::output
Output * output
Definition: Node.h:182
Output
Definition: Output.h:43
END_OF_RUN
#define END_OF_RUN
Definition: Output.h:26
void SimParameters::close_veldcdfile ( )

Definition at line 664 of file Output.C.

References END_OF_RUN, Node::Object(), and Node::output.

664  {
665 
666  Output *output = Node::Object()->output;
667  if ( ! output ) return;
668 
669  output->output_veldcdfile(END_OF_RUN, 0, 0);
670 
671 }
Node::Object
static Node * Object()
Definition: Node.h:86
Node::output
Output * output
Definition: Node.h:182
Output
Definition: Output.h:43
END_OF_RUN
#define END_OF_RUN
Definition: Output.h:26
BigReal SimParameters::getBondLambda ( const BigReal  lambda)

Definition at line 7267 of file SimParameters.C.

Referenced by Controller::computeAlchWork(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), and Controller::outputTiEnergy().

7267  {
7268  // Convenience function for staggered lambda scaling
7269  return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
7270 }
SimParameters::alchBondLambdaEnd
BigReal alchBondLambdaEnd
Definition: SimParameters.h:430
BigReal SimParameters::getCurrentLambda ( const int  step)

Definition at line 7188 of file SimParameters.C.

Referenced by Controller::calcPressure(), Controller::computeAlchWork(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), Controller::printEnergies(), and ComputePme::ungridForces().

7188  {
7189  /*Get lambda at the current step.
7190 
7191  If alchLambdaFreq = 0, return alchLambda. For positive values of
7192  alchLambdaFreq, apply a linear stepwise schedule from alchLambda to
7193  alchLambda2:
7194 
7195  l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
7196 
7197  n - the current time step
7198  n0 - step at which switching begins (default = 0)
7199  N - total steps in the simulation
7200  dn - alchLambdaFreq (increment frequency, in steps)
7201  l/l2 - alchLambda/alchLambda2
7202 
7203  Note that each step _begins_ by incrementing alchLambda and then integrates
7204  in time. This means that the first and last switch steps may not behave as
7205  immediately expected - at step 0, alchLambda is NOT evaluated and at step N
7206  no step occurs because alchLambda2 has already been reached.
7207  */
7208  if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
7209  if ( step == N ) {
7210  return alchLambda2;
7211  }
7212  else {
7213  const int timeOrigin = firstTimestep + alchEquilSteps;
7214  const BigReal alchLambdaDelta = getLambdaDelta();
7215  const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
7216  return alchLambda + alchLambdaDelta*(floor(increment) + 1);
7217  }
7218  }
7219  else {
7220  return alchLambda;
7221  }
7222 }
SimParameters::getLambdaDelta
BigReal getLambdaDelta(void)
Definition: SimParameters.C:7224
SimParameters::alchLambda2
BigReal alchLambda2
Definition: SimParameters.h:397
SimParameters::alchLambda
BigReal alchLambda
Definition: SimParameters.h:396
BigReal
double BigReal
Definition: common.h:114
BigReal SimParameters::getCurrentLambda2 ( const int  step)

Definition at line 7147 of file SimParameters.C.

Referenced by AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), Controller::outputTiEnergy(), Controller::printEnergies(), and ComputePme::ungridForces().

7147  {
7148  if ( alchLambdaIDWS >= 0. ) {
7149  const BigReal lambda2 = ( (step / alchIDWSFreq) % 2 == 1 ) ? alchLambda2 : alchLambdaIDWS;
7150  return lambda2;
7151  } else {
7152  return alchLambda2;
7153  }
7154 }
SimParameters::alchLambda2
BigReal alchLambda2
Definition: SimParameters.h:397
SimParameters::alchLambdaIDWS
BigReal alchLambdaIDWS
Definition: SimParameters.h:398
BigReal
double BigReal
Definition: common.h:114
BigReal SimParameters::getElecLambda ( const BigReal  lambda)

Definition at line 7230 of file SimParameters.C.

Referenced by Controller::computeAlchWork(), TholeElem::computeForce(), Controller::outputTiEnergy(), ComputePmeMgr::submitReductions(), and ComputePme::ungridForces().

7230  {
7231  // Convenience function for staggered lambda scaling
7232  return (lambda <= alchElecLambdaStart ? 0.
7233  : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
7234 }
SimParameters::alchElecLambdaStart
BigReal alchElecLambdaStart
Definition: SimParameters.h:413
char * SimParameters::getfromparseopts ( const char *  name,
char *  outbuf 
)

Definition at line 104 of file SimParameters.C.

104  {
105  if ( parseopts ) return parseopts->getfromptr(name,outbuf);
106  else return 0;
107 }
ParseOptions::getfromptr
char * getfromptr(const char *name, char *outbuf)
Definition: ParseOptions.C:938
BigReal SimParameters::getLambdaDelta ( void  )

Definition at line 7224 of file SimParameters.C.

Referenced by Controller::outputTiEnergy().

7224  {
7225  // Increment by which Lambda changes.
7226  return ((alchLambda2 - alchLambda)*alchLambdaFreq
7227  / BigReal(N - firstTimestep - alchEquilSteps));
7228 }
SimParameters::alchLambda2
BigReal alchLambda2
Definition: SimParameters.h:397
SimParameters::alchLambda
BigReal alchLambda
Definition: SimParameters.h:396
BigReal
double BigReal
Definition: common.h:114
BigReal SimParameters::getRepLambda ( const BigReal  lambda)

Definition at line 7262 of file SimParameters.C.

7262  {
7263  // Convenience function for staggered lambda scaling
7264  return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd);
7265 }
SimParameters::alchRepLambdaEnd
BigReal alchRepLambdaEnd
Definition: SimParameters.h:424
BigReal SimParameters::getVdwLambda ( const BigReal  lambda)

Definition at line 7244 of file SimParameters.C.

Referenced by Controller::computeAlchWork(), and Controller::outputTiEnergy().

7244  {
7245  // Convenience function for staggered lambda scaling
7246  if ( alchWCAOn ) {
7247  // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart.
7248  // The second condition is needed when attractive interactions are inactive
7249  // for the whole range, otherwise lambda = 0/1 are incorrect.
7250  if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) {
7251  return 0.0;
7252  } else if ( lambda >= alchVdwLambdaEnd ) {
7253  return 1.0;
7254  } else {
7255  return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd);
7256  }
7257  } else {
7258  return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
7259  }
7260 }
SimParameters::alchRepLambdaEnd
BigReal alchRepLambdaEnd
Definition: SimParameters.h:424
SimParameters::alchVdwLambdaEnd
BigReal alchVdwLambdaEnd
Definition: SimParameters.h:419
void SimParameters::initialize_config_data ( ConfigList *  config,
char *&  cwd 
)

Definition at line 132 of file SimParameters.C.

References ParseOptions::check_consistency(), NAMD_die(), and ParseOptions::set().

Referenced by SimParameters().

134 {
135 
136  parseopts = new ParseOptions; // Object to check consistency of config file
137  ParseOptions &opts = *parseopts;
138 
139  config_parser(opts);
140 
142  if (!opts.check_consistency())
143  {
144  NAMD_die("Internal error in configuration file parser");
145  }
146 
147  // Now, feed the object with the actual configuration options through the
148  // ParseOptions file and make sure everything is OK
149  if (!opts.set(*config))
150  {
151  NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
152  }
153 
155 
156  check_config(opts,config,cwd);
157 
158  print_config(opts,config,cwd);
159 
160 }
ParseOptions::set
Bool set(const ConfigList &configlist)
Definition: ParseOptions.C:642
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:85
ParseOptions::check_consistency
Bool check_consistency(void)
Definition: ParseOptions.C:391
int SimParameters::isRecvSpanningTreeOn ( )
inline

Definition at line 1086 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

1086 { return proxyRecvSpanningTree == 1; }
int SimParameters::isRecvSpanningTreeUnset ( )
inline

Definition at line 1087 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().

1087 { return proxyRecvSpanningTree == -1; }
int SimParameters::isSendSpanningTreeOn ( )
inline

Definition at line 1084 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

1084 { return proxySendSpanningTree == 1; }
int SimParameters::isSendSpanningTreeUnset ( )
inline

Definition at line 1085 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().

1085 { return proxySendSpanningTree == -1; }
int SimParameters::issetinparseopts ( const char *  name)

Definition at line 114 of file SimParameters.C.

114  {
115  if ( parseopts ) return parseopts->issetfromptr(name);
116  else return -1;
117 }
ParseOptions::issetfromptr
int issetfromptr(const char *name)
Definition: ParseOptions.C:987
int SimParameters::istrueinparseopts ( const char *  name)

Definition at line 109 of file SimParameters.C.

109  {
110  if ( parseopts ) return parseopts->istruefromptr(name);
111  else return -1;
112 }
ParseOptions::istruefromptr
int istruefromptr(const char *name)
Definition: ParseOptions.C:976
void SimParameters::nonbonded_select ( )
static

Definition at line 398 of file SimParameters.C.

References ComputeNonbondedUtil::select().

Referenced by Node::resendMolecule(), and Node::startup().

398  {
399  ComputeNonbondedUtil::select();
400 }
ComputeNonbondedUtil::select
static void select(void)
Definition: ComputeNonbondedUtil.C:253
void SimParameters::pme_select ( )
static

Definition at line 402 of file SimParameters.C.

References ComputePmeUtil::select().

Referenced by Node::resendMolecule(), and Node::startup().

402  {
403  ComputePmeUtil::select();
404 }
ComputePmeUtil::select
static void select(void)
Definition: ComputePme.C:6364
void SimParameters::readExtendedSystem ( const char *  filename,
Lattice *  latptr = 0 
)

Definition at line 2341 of file SimParameters.C.

References Lattice::a_p(), Lattice::b_p(), Lattice::c_p(), endi(), iINFO(), iout, NAMD_die(), and Lattice::set().

2341  {
2342 
2343  if ( ! latptr ) {
2344  iout << iINFO << "EXTENDED SYSTEM FILE " << filename << "\n" << endi;
2345  }
2346 
2347  ifstream xscFile(filename);
2348  if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
2349 
2350  char labels[1024];
2351  do {
2352  if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
2353  xscFile.getline(labels,1023);
2354  } while ( strncmp(labels,"#$LABELS ",9) );
2355 
2356  int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
2357  a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
2358  int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
2359  o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
2360 
2361  int pos = 0;
2362  char *l_i = labels + 8;
2363  while ( *l_i ) {
2364  if ( *l_i == ' ' ) { ++l_i; continue; }
2365  char *l_i2;
2366  for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
2367  if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
2368  if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
2369  if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
2370  if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
2371  if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
2372  if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
2373  if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
2374  if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
2375  if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
2376  if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
2377  if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
2378  if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
2379  if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
2380  if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
2381  if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
2382  if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
2383  if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
2384  if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
2385  if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
2386  }
2387  ++pos;
2388  l_i = l_i2;
2389  }
2390  int numpos = pos;
2391 
2392  for ( pos = 0; pos < numpos; ++pos ) {
2393  double tmp;
2394  xscFile >> tmp;
2395  if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
2396  if ( pos == a_x ) cellBasisVector1.x = tmp;
2397  if ( pos == a_y ) cellBasisVector1.y = tmp;
2398  if ( pos == a_z ) cellBasisVector1.z = tmp;
2399  if ( pos == b_x ) cellBasisVector2.x = tmp;
2400  if ( pos == b_y ) cellBasisVector2.y = tmp;
2401  if ( pos == b_z ) cellBasisVector2.z = tmp;
2402  if ( pos == c_x ) cellBasisVector3.x = tmp;
2403  if ( pos == c_y ) cellBasisVector3.y = tmp;
2404  if ( pos == c_z ) cellBasisVector3.z = tmp;
2405  if ( pos == o_x ) cellOrigin.x = tmp;
2406  if ( pos == o_y ) cellOrigin.y = tmp;
2407  if ( pos == o_z ) cellOrigin.z = tmp;
2408  if ( pos == s_u ) strainRate2.x = tmp;
2409  if ( pos == s_v ) strainRate2.y = tmp;
2410  if ( pos == s_w ) strainRate2.z = tmp;
2411  if ( pos == s_x ) strainRate.x = tmp;
2412  if ( pos == s_y ) strainRate.y = tmp;
2413  if ( pos == s_z ) strainRate.z = tmp;
2414  }
2415 
2416  if ( latptr ) {
2417  Lattice test;
2418  test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
2419 
2420  if ( test.a_p() && ! lattice.a_p() ) {
2421  NAMD_die("cellBasisVector1 added during atom reinitialization");
2422  }
2423  if ( lattice.a_p() && ! test.a_p() ) {
2424  NAMD_die("cellBasisVector1 dropped during atom reinitialization");
2425  }
2426  if ( test.b_p() && ! lattice.b_p() ) {
2427  NAMD_die("cellBasisVector2 added during atom reinitialization");
2428  }
2429  if ( lattice.b_p() && ! test.b_p() ) {
2430  NAMD_die("cellBasisVector2 dropped during atom reinitialization");
2431  }
2432  if ( test.c_p() && ! lattice.c_p() ) {
2433  NAMD_die("cellBasisVector3 added during atom reinitialization");
2434  }
2435  if ( lattice.c_p() && ! test.c_p() ) {
2436  NAMD_die("cellBasisVector3 dropped during atom reinitialization");
2437  }
2438 
2439  latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
2440  }
2441 
2442 }
iINFO
std::ostream & iINFO(std::ostream &s)
Definition: InfoStream.C:81
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
Vector::z
BigReal z
Definition: Vector.h:66
SimParameters::cellBasisVector1
zVector cellBasisVector1
Definition: SimParameters.h:127
iout
#define iout
Definition: InfoStream.h:51
SimParameters::cellBasisVector3
zVector cellBasisVector3
Definition: SimParameters.h:129
Lattice::set
void set(Vector A, Vector B, Vector C)
Definition: Lattice.h:31
SimParameters::strainRate2
zVector strainRate2
Definition: SimParameters.h:716
Vector::x
BigReal x
Definition: Vector.h:66
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:85
SimParameters::strainRate
zVector strainRate
Definition: SimParameters.h:715
SimParameters::cellBasisVector2
zVector cellBasisVector2
Definition: SimParameters.h:128
Vector::y
BigReal y
Definition: Vector.h:66
Lattice::b_p
int b_p() const
Definition: Lattice.h:274
Lattice::a_p
int a_p() const
Definition: Lattice.h:273
SimParameters::cellOrigin
zVector cellOrigin
Definition: SimParameters.h:130
Lattice::c_p
int c_p() const
Definition: Lattice.h:275
void SimParameters::receive_SimParameters ( MIStream *  msg)

Definition at line 7088 of file SimParameters.C.

References MIStream::get().

7090 {
7091  msg->get(sizeof(SimParameters),(char*)this);
7092  if ( FFTWWisdomString ) {
7093  int fftwlen;
7094  msg->get(fftwlen);
7095  FFTWWisdomString = new char[fftwlen];
7096  msg->get(fftwlen,FFTWWisdomString);
7097 #ifdef NAMD_FFTW
7098 #ifdef NAMD_FFTW_3
7099  fftwf_import_wisdom_from_string(FFTWWisdomString);
7100 #else
7101  fftw_import_wisdom_from_string(FFTWWisdomString);
7102 #endif
7103 #endif
7104  }
7105  if ( tclBCScript ) {
7106  int tcllen;
7107  msg->get(tcllen);
7108  tclBCScript = new char[tcllen];
7109  msg->get(tcllen,tclBCScript);
7110  }
7111 
7112 #ifdef MEM_OPT_VERSION
7113  int filelen;
7114  msg->get(filelen);
7115  binAtomFile = new char[filelen];
7116  msg->get(filelen, binAtomFile);
7117 
7118  msg->get(filelen);
7119  binCoorFile = new char[filelen];
7120  msg->get(filelen, binCoorFile);
7121 
7122  if(binVelFile) {
7123  msg->get(filelen);
7124  binVelFile = new char[filelen];
7125  msg->get(filelen, binVelFile);
7126  }
7127 
7128  if(binRefFile) {
7129  msg->get(filelen);
7130  binRefFile = new char[filelen];
7131  msg->get(filelen, binRefFile);
7132  }
7133 #endif
7134 
7135 
7136  // The simParameters bit copy above put illegal values in the list pointers
7137  // So this resets everything so that unpacking will work.
7138  mgridforcelist.clear();
7139  mgridforcelist.unpack_data(msg);
7140 
7141  delete msg;
7142 }
SimParameters::FFTWWisdomString
char * FFTWWisdomString
Definition: SimParameters.h:821
SimParameters::tclBCScript
char * tclBCScript
Definition: SimParameters.h:557
MIStream::get
MIStream * get(char &data)
Definition: MStream.h:29
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:277
MGridforceParamsList::unpack_data
void unpack_data(MIStream *msg)
Definition: MGridforceParams.C:162
void SimParameters::scriptSet ( const char *  param,
const char *  value 
)

Definition at line 174 of file SimParameters.C.

References atobool(), ComputeCUDAMgr::getComputeCUDAMgr(), MAX_SCRIPT_PARAM_SIZE, NAMD_die(), PRESSUREFACTOR, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_MOD_FLOAT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, ComputePmeUtil::select(), ComputeNonbondedUtil::select(), and ComputeCUDAMgr::update().

Referenced by Node::scriptParam().

174  {
175 
176  if ( CkMyRank() ) return;
177 
178 #define MAX_SCRIPT_PARAM_SIZE 128
179 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
180 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
181 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
182 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
183 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
184 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
185 
186  SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
187  SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
188  SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
189  SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
190  SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
191  SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1)
192  SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2)
193  SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1)
194  SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2)
195  SCRIPT_PARSE_INT("numsteps",N)
196  if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) {
197  N = firstTimestep = atoi(value); return;
198  }
199  SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
200  SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
201  SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
202  SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
203  // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
204  if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) {
205  langevinOn = atobool(value);
206  if ( langevinOn && ! langevinOnAtStartup ) {
207  NAMD_die("Langevin must be enabled at startup to disable and re-enable in script.");
208  }
209  return;
210  }
211  SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
212  SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
213  SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
214  SCRIPT_PARSE_BOOL("stochRescale",stochRescaleOn)
215  SCRIPT_PARSE_FLOAT("stochRescaleTemp",stochRescaleTemp)
216  SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
217  SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
218  SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
219  SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
220  SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
221  SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
222  SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
223  SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
224  SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
225  SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
226  SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
227  langevinPistonTarget,/PRESSUREFACTOR)
228  SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
229  SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
230  SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
231  SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
232  surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
233  SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
234  SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
235  berendsenPressureTarget,/PRESSUREFACTOR)
236  SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
237  berendsenPressureCompressibility,*PRESSUREFACTOR)
238  SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
239  berendsenPressureRelaxationTime)
240  SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
241  SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
242  SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn)
243  SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst)
244  SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen)
245  SCRIPT_PARSE_STRING("outputname",outputFilename)
246  SCRIPT_PARSE_INT("outputEnergies",outputEnergies)
247  SCRIPT_PARSE_INT("outputEnergiesPrecision",outputEnergiesPrecision)
248  SCRIPT_PARSE_STRING("restartname",restartFilename)
249  SCRIPT_PARSE_INT("DCDfreq",dcdFrequency)
250  if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) {
251  close_dcdfile(); // *** implemented in Output.C ***
252  strcpy(dcdFilename,value);
253  return;
254  }
255  if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) {
256  close_veldcdfile(); // *** implemented in Output.C ***
257  strcpy(velDcdFilename,value);
258  return;
259  }
260  SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
261  SCRIPT_PARSE_VECTOR("eField",eField)
262  SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
263  SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase)
264  SCRIPT_PARSE_FLOAT("accelMDE",accelMDE)
265  SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha)
266  SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE)
267  SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha)
268  SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P)
269  SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D)
270  SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile)
271  SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
272  SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
273  if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
274  NAMD_die("Can't yet modify mgridforcescale in a script");
275  return;
276  }
277  if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
278  NAMD_die("Can't yet modify mgridforcevoff in a script");
279  return;
280  }
281 
282  if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
283  if ( ! fixedAtomsOn )
284  NAMD_die("FixedAtoms may not be enabled in a script.");
285  if ( ! fixedAtomsForces )
286  NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
287  fixedAtomsOn = atobool(value);
288  return;
289  }
290 
291 //fepb
292  if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) {
293  alchOn = atobool(value);
294  if ( alchOn && ! alchOnAtStartup ) {
295  NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script.");
296  }
297  alchFepOn = alchOn && alchFepOnAtStartup;
298  alchThermIntOn = alchOn && alchThermIntOnAtStartup;
299  ComputeNonbondedUtil::select();
300  if ( PMEOn ) ComputePmeUtil::select();
301  return;
302  }
303  SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
304 
305  if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
306  alchLambda = atof(value);
307  if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
308  NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
309  }
310  ComputeNonbondedUtil::select();
311  return;
312  }
313 
314  if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
315  alchLambda2 = atof(value);
316  if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
317  NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
318  }
319  ComputeNonbondedUtil::select();
320  return;
321  }
322 
323  if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
324  alchLambdaIDWS = atof(value);
325  setupIDWS();
326  ComputeNonbondedUtil::select();
327  return;
328  }
329 
330  if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
331  alchLambdaFreq = atoi(value);
332  if ( alchLambdaIDWS >= 0 ) {
333  NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n");
334  }
335  ComputeNonbondedUtil::select();
336  return;
337  }
338 //fepe
339 
340  if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
341  nonbondedScaling = atof(value);
342  ComputeNonbondedUtil::select();
343  return;
344  }
345 
346  if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
347  commOnly = atobool(value);
348  ComputeNonbondedUtil::select();
349  return;
350  }
351 
352  // REST2 - We don't have to make any changes to ComputeNonbondedUtil
353  // other than recalculating the LJTable. Skip doing the other stuff.
354  if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) {
355  soluteScalingFactor = atof(value);
356  if (soluteScalingFactor < 0.0) {
357  NAMD_die("Solute scaling factor should be non-negative\n");
358  }
359  soluteScalingFactorCharge = soluteScalingFactor;
360  soluteScalingFactorVdw = soluteScalingFactor;
361  // update LJTable for CPU
362  ComputeNonbondedUtil::select();
363 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
364  // update LJTable for GPU, needs CPU update first
365  ComputeCUDAMgr::getComputeCUDAMgr()->update();
366 #endif
367  return;
368  }
369  if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) {
370  soluteScalingFactorVdw = atof(value);
371  if (soluteScalingFactorVdw < 0.0) {
372  NAMD_die("Solute scaling factor for van der Waals "
373  "should be non-negative\n");
374  }
375  // update LJTable for CPU
376  ComputeNonbondedUtil::select();
377 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
378  // update LJTable for GPU, needs CPU update first
379  ComputeCUDAMgr::getComputeCUDAMgr()->update();
380 #endif
381  return;
382  }
383  if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) {
384  soluteScalingFactorCharge = atof(value);
385  if (soluteScalingFactorCharge < 0.0) {
386  NAMD_die("Solute scaling factor for electrostatics "
387  "should be non-negative\n");
388  }
389  return;
390  }
391 
392  char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
393  sprintf(error,"Setting parameter %s from script failed!\n",param);
394  NAMD_die(error);
395 
396 }
SimParameters::berendsenPressureCompressibility
BigReal berendsenPressureCompressibility
Definition: SimParameters.h:684
SimParameters::berendsenPressureOn
Bool berendsenPressureOn
Definition: SimParameters.h:682
SimParameters::scriptArg3
BigReal scriptArg3
Definition: SimParameters.h:1008
SimParameters::scriptStringArg1
char scriptStringArg1[128]
Definition: SimParameters.h:1013
SimParameters::berendsenPressureRelaxationTime
BigReal berendsenPressureRelaxationTime
Definition: SimParameters.h:685
SimParameters::soluteScalingFactorCharge
BigReal soluteScalingFactorCharge
Definition: SimParameters.h:450
SimParameters::scriptArg2
BigReal scriptArg2
Definition: SimParameters.h:1007
SimParameters::scriptStringArg2
char scriptStringArg2[128]
Definition: SimParameters.h:1014
SimParameters::accelMDE
BigReal accelMDE
Definition: SimParameters.h:624
SimParameters::langevinPistonTemp
BigReal langevinPistonTemp
Definition: SimParameters.h:693
SimParameters::close_veldcdfile
void close_veldcdfile()
Definition: Output.C:664
SimParameters::eFieldFreq
BigReal eFieldFreq
Definition: SimParameters.h:864
SimParameters::scriptArg5
BigReal scriptArg5
Definition: SimParameters.h:1010
PRESSUREFACTOR
#define PRESSUREFACTOR
Definition: common.h:49
SimParameters::nonbondedScaling
BigReal nonbondedScaling
Definition: SimParameters.h:201
atobool
int atobool(const char *s)
Definition: SimParameters.C:168
SimParameters::constraintScaling
BigReal constraintScaling
Definition: SimParameters.h:291
SimParameters::velDcdFilename
char velDcdFilename[NAMD_FILENAME_BUFFER_SIZE]
Definition: SimParameters.h:213
SimParameters::surfaceTensionTarget
BigReal surfaceTensionTarget
Definition: SimParameters.h:704
SimParameters::reassignTemp
BigReal reassignTemp
Definition: SimParameters.h:664
SimParameters::alchLambda2
BigReal alchLambda2
Definition: SimParameters.h:397
SimParameters::accelMDTE
BigReal accelMDTE
Definition: SimParameters.h:626
SCRIPT_PARSE_VECTOR
#define SCRIPT_PARSE_VECTOR(NAME, VAR)
if
if(ComputeNonbondedUtil::goMethod==2)
Definition: ComputeNonbondedBase2.h:434
SimParameters::stirPivot
zVector stirPivot
Definition: SimParameters.h:874
SimParameters::accelMDalpha
BigReal accelMDalpha
Definition: SimParameters.h:625
SimParameters::alchLambda
BigReal alchLambda
Definition: SimParameters.h:396
SimParameters::close_dcdfile
void close_dcdfile()
Definition: Output.C:655
SimParameters::outputFilename
char outputFilename[NAMD_FILENAME_BUFFER_SIZE]
Definition: SimParameters.h:216
SimParameters::langevinOnAtStartup
Bool langevinOnAtStartup
Definition: SimParameters.h:567
MAX_SCRIPT_PARAM_SIZE
#define MAX_SCRIPT_PARAM_SIZE
SimParameters::eFieldPhase
BigReal eFieldPhase
Definition: SimParameters.h:865
SimParameters::accelMDTalpha
BigReal accelMDTalpha
Definition: SimParameters.h:627
SimParameters::tclBCArgs
char tclBCArgs[NAMD_FILENAME_BUFFER_SIZE]
Definition: SimParameters.h:558
SimParameters::langevinPistonDecay
BigReal langevinPistonDecay
Definition: SimParameters.h:692
SimParameters::alchLambdaIDWS
BigReal alchLambdaIDWS
Definition: SimParameters.h:398
SimParameters::stirAxis
zVector stirAxis
Definition: SimParameters.h:873
SimParameters::langevin_useBAOAB
Bool langevin_useBAOAB
Definition: SimParameters.h:572
SimParameters::berendsenPressureTarget
BigReal berendsenPressureTarget
Definition: SimParameters.h:683
SCRIPT_PARSE_STRING
#define SCRIPT_PARSE_STRING(NAME, VAR)
SCRIPT_PARSE_INT
#define SCRIPT_PARSE_INT(NAME, VAR)
SimParameters::rescaleTemp
BigReal rescaleTemp
Definition: SimParameters.h:615
ComputeCUDAMgr::getComputeCUDAMgr
static ComputeCUDAMgr * getComputeCUDAMgr()
Definition: ComputeCUDAMgr.C:83
SimParameters::soluteScalingFactor
BigReal soluteScalingFactor
Definition: SimParameters.h:448
SimParameters::dcdFilename
char dcdFilename[NAMD_FILENAME_BUFFER_SIZE]
Definition: SimParameters.h:212
SimParameters::drudeBondLen
BigReal drudeBondLen
Definition: SimParameters.h:540
SimParameters::langevinTemp
BigReal langevinTemp
Definition: SimParameters.h:569
SimParameters::scriptArg1
BigReal scriptArg1
Definition: SimParameters.h:1006
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:85
SimParameters::soluteScalingFactorVdw
BigReal soluteScalingFactorVdw
Definition: SimParameters.h:453
ComputeNonbondedUtil::select
static void select(void)
Definition: ComputeNonbondedUtil.C:253
SimParameters::drudeBondConst
BigReal drudeBondConst
Definition: SimParameters.h:542
SimParameters::accelMDGSigma0P
BigReal accelMDGSigma0P
Definition: SimParameters.h:636
SimParameters::restartFilename
char restartFilename[NAMD_FILENAME_BUFFER_SIZE]
Definition: SimParameters.h:221
SimParameters::langevinPistonPeriod
BigReal langevinPistonPeriod
Definition: SimParameters.h:691
SimParameters::alchFepOnAtStartup
Bool alchFepOnAtStartup
Definition: SimParameters.h:387
SimParameters::initialTemp
BigReal initialTemp
Definition: SimParameters.h:187
SimParameters::scriptArg4
BigReal scriptArg4
Definition: SimParameters.h:1009
SimParameters::accelMDGRestartFile
char accelMDGRestartFile[NAMD_FILENAME_BUFFER_SIZE]
Definition: SimParameters.h:639
SimParameters::alchThermIntOnAtStartup
Bool alchThermIntOnAtStartup
Definition: SimParameters.h:388
SCRIPT_PARSE_BOOL
#define SCRIPT_PARSE_BOOL(NAME, VAR)
ComputePmeUtil::select
static void select(void)
Definition: ComputePme.C:6364
SimParameters::maximumMove
BigReal maximumMove
Definition: SimParameters.h:833
SimParameters::accelMDGSigma0D
BigReal accelMDGSigma0D
Definition: SimParameters.h:637
SCRIPT_PARSE_MOD_FLOAT
#define SCRIPT_PARSE_MOD_FLOAT(NAME, VAR, MOD)
SimParameters::langevinPistonTarget
BigReal langevinPistonTarget
Definition: SimParameters.h:690
SimParameters::outputEnergiesPrecision
int outputEnergiesPrecision
Definition: SimParameters.h:887
SimParameters::stochRescaleTemp
BigReal stochRescaleTemp
Definition: SimParameters.h:600
SimParameters::consForceScaling
BigReal consForceScaling
Definition: SimParameters.h:882
SimParameters::loweAndersenTemp
BigReal loweAndersenTemp
Definition: SimParameters.h:577
SCRIPT_PARSE_FLOAT
#define SCRIPT_PARSE_FLOAT(NAME, VAR)
void SimParameters::send_SimParameters ( MOStream *  msg)

Definition at line 7030 of file SimParameters.C.

References MOStream::end(), and MOStream::put().

7032 {
7033  /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
7034  if ( msg == NULL )
7035  {
7036  NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
7037  }*/
7038 
7039  msg->put(sizeof(SimParameters),(char*)this);
7040  if ( FFTWWisdomString ) {
7041  int fftwlen = strlen(FFTWWisdomString) + 1;
7042  msg->put(fftwlen);
7043  msg->put(fftwlen,FFTWWisdomString);
7044  }
7045  if ( tclBCScript ) {
7046  int tcllen = strlen(tclBCScript) + 1;
7047  msg->put(tcllen);
7048  msg->put(tcllen,tclBCScript);
7049  }
7050 
7051 #ifdef MEM_OPT_VERSION
7052  int filelen = strlen(binAtomFile)+1;
7053  msg->put(filelen);
7054  msg->put(filelen, binAtomFile);
7055 
7056  filelen = strlen(binCoorFile)+1;
7057  msg->put(filelen);
7058  msg->put(filelen, binCoorFile);
7059 
7060  if(binVelFile) {
7061  filelen = strlen(binVelFile)+1;
7062  msg->put(filelen);
7063  msg->put(filelen, binVelFile);
7064  }
7065 
7066  if(binRefFile) {
7067  filelen = strlen(binRefFile)+1;
7068  msg->put(filelen);
7069  msg->put(filelen, binRefFile);
7070  }
7071 #endif
7072 
7073  mgridforcelist.pack_data(msg);
7074 
7075  msg->end();
7076 }
MOStream::end
void end(void)
Definition: MStream.C:176
SimParameters::FFTWWisdomString
char * FFTWWisdomString
Definition: SimParameters.h:821
SimParameters::tclBCScript
char * tclBCScript
Definition: SimParameters.h:557
SimParameters::mgridforcelist
MGridforceParamsList mgridforcelist
Definition: SimParameters.h:277
MOStream::put
MOStream * put(char data)
Definition: MStream.h:112
MGridforceParamsList::pack_data
void pack_data(MOStream *msg)
Definition: MGridforceParams.C:106
int SimParameters::setupIDWS ( )

Definition at line 7157 of file SimParameters.C.

References endi(), iout, iWARN(), and NAMD_die().

7157  {
7158  if (alchLambdaIDWS < 0.) return 0;
7159  if (alchLambdaIDWS > 1.) {
7160  NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
7161  }
7162  /*
7163  * The internal parameter alchIDWSFreq determines the number of steps of MD
7164  * before each switch of the value of alchLambda2. At most this occurs every
7165  * time the energy is evaluated and thus the default is the greater of
7166  * fullElectFrequency and nonbondedFrequency. However, this choice fails to
7167  * report alternating values if output is printed less often than every step
7168  * (which is almost certainly true). Thus the frequency is reset to match
7169  * alchOutFreq or, if that is zero, outputEnergies. Note that, if
7170  * alchOutFreq > 0 but != outputEnergies, then the data going to stdout
7171  * are likely not useful since the comparison value is difficult to infer.
7172  */
7173  if ( alchOutFreq % fullElectFrequency != 0 ) {
7174  NAMD_die("For IDWS, alchOutFreq must be a multiple of fullElectFrequency.\n");
7175  }
7176  alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency;
7177  if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies;
7178  if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq;
7179  if ( alchOutFreq && alchOutFreq != outputEnergies) {
7180  iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput"
7181  << " to stdout may not be useful!\n" << endi;
7182  }
7183  return 1;
7184 }
endi
std::ostream & endi(std::ostream &s)
Definition: InfoStream.C:54
iWARN
std::ostream & iWARN(std::ostream &s)
Definition: InfoStream.C:82
iout
#define iout
Definition: InfoStream.h:51
SimParameters::alchLambdaIDWS
BigReal alchLambdaIDWS
Definition: SimParameters.h:398
NAMD_die
void NAMD_die(const char *err_msg)
Definition: common.C:85

Member Data Documentation

int SimParameters::aaAngleExp

Definition at line 973 of file SimParameters.h.

BigReal SimParameters::accelMDalpha

Definition at line 625 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDDebugOn

Definition at line 620 of file SimParameters.h.

Referenced by Controller::receivePressure(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().

Bool SimParameters::accelMDdihe

Definition at line 618 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().

Bool SimParameters::accelMDdual

Definition at line 619 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().

BigReal SimParameters::accelMDE

Definition at line 624 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDFirstStep

Definition at line 621 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDG

Definition at line 629 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDPrepSteps

Definition at line 633 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDSteps

Definition at line 631 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiPrepSteps

Definition at line 634 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiSteps

Definition at line 632 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGiE

Definition at line 630 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGresetVaftercmd

Definition at line 640 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGRestart

Definition at line 638 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

char SimParameters::accelMDGRestartFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 639 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDGSigma0D

Definition at line 637 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDGSigma0P

Definition at line 636 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGStatWindow

Definition at line 635 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDLastStep

Definition at line 622 of file SimParameters.h.

Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().

Bool SimParameters::accelMDOn

Definition at line 617 of file SimParameters.h.

Referenced by Controller::calcPressure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), Sequencer::integrate(), Controller::receivePressure(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().

int SimParameters::accelMDOutFreq

Definition at line 623 of file SimParameters.h.

Referenced by Controller::receivePressure(), and Controller::rescaleaccelMD().

BigReal SimParameters::accelMDTalpha

Definition at line 627 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDTE

Definition at line 626 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::adaptTempAutoDt

Definition at line 651 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempBins

Definition at line 652 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempCgamma

Definition at line 654 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempDebug

Definition at line 644 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

BigReal SimParameters::adaptTempDt

Definition at line 653 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempFirstStep

Definition at line 645 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

int SimParameters::adaptTempFreq

Definition at line 648 of file SimParameters.h.

Referenced by Sequencer::adaptTempUpdate(), and Controller::adaptTempUpdate().

char SimParameters::adaptTempInFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 657 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempLangevin

Definition at line 655 of file SimParameters.h.

Referenced by Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2().

int SimParameters::adaptTempLastStep

Definition at line 646 of file SimParameters.h.

Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities().

Bool SimParameters::adaptTempOn

Definition at line 643 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and Controller::rescaleVelocities().

int SimParameters::adaptTempOutFreq

Definition at line 647 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRandom

Definition at line 660 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRescale

Definition at line 656 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

char SimParameters::adaptTempRestartFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 658 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempRestartFreq

Definition at line 659 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), and Controller::adaptTempWriteRestart().

BigReal SimParameters::adaptTempTmax

Definition at line 650 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempTmin

Definition at line 649 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::alchBondDecouple

Definition at line 436 of file SimParameters.h.

Referenced by CrosstermElem::computeForce().

BigReal SimParameters::alchBondLambdaEnd

Definition at line 430 of file SimParameters.h.

Bool SimParameters::alchDecouple

Definition at line 435 of file SimParameters.h.

Referenced by TholeElem::computeForce(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().

BigReal SimParameters::alchElecLambdaStart

Definition at line 413 of file SimParameters.h.

Referenced by ComputePmeUtil::select().

Bool SimParameters::alchEnsembleAvg

Definition at line 408 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().

int SimParameters::alchEquilSteps

Definition at line 410 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), and Controller::printTiMessage().

Bool SimParameters::alchFepOn

Definition at line 390 of file SimParameters.h.

Referenced by ComputePmeCUDA::initialize(), Controller::outputFepEnergy(), Controller::printEnergies(), Controller::printFepMessage(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().

Bool SimParameters::alchFepOnAtStartup

Definition at line 387 of file SimParameters.h.

int SimParameters::alchIDWSFreq

Definition at line 399 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().

BigReal SimParameters::alchLambda

Definition at line 396 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), and Controller::writeFepEnergyData().

BigReal SimParameters::alchLambda2

Definition at line 397 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), and Controller::printFepMessage().

int SimParameters::alchLambdaFreq

Definition at line 400 of file SimParameters.h.

Referenced by Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), and Controller::writeTiEnergyData().

BigReal SimParameters::alchLambdaIDWS

Definition at line 398 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), and Controller::writeFepEnergyData().

int SimParameters::alchMethod

Definition at line 395 of file SimParameters.h.

Bool SimParameters::alchOn

Definition at line 389 of file SimParameters.h.

Referenced by AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), Molecule::receive_Molecule(), ComputePmeUtil::select(), and Molecule::send_Molecule().

Bool SimParameters::alchOnAtStartup

Definition at line 386 of file SimParameters.h.

char SimParameters::alchOutFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 409 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().

int SimParameters::alchOutFreq

Definition at line 407 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().

BigReal SimParameters::alchRepLambdaEnd

Definition at line 424 of file SimParameters.h.

BigReal SimParameters::alchTemp

Definition at line 406 of file SimParameters.h.

Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), and Controller::writeFepEnergyData().

Bool SimParameters::alchThermIntOn

Definition at line 393 of file SimParameters.h.

Referenced by ComputePmeCUDA::initialize(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiMessage(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().

Bool SimParameters::alchThermIntOnAtStartup

Definition at line 388 of file SimParameters.h.

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 419 of file SimParameters.h.

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 411 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::alchWCAOn

Definition at line 394 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::alpha_cutoff

Definition at line 530 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().

BigReal SimParameters::alpha_max

Definition at line 531 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), and HomePatch::gbisComputeAfterP1().

Bool SimParameters::amberOn

Definition at line 994 of file SimParameters.h.

Referenced by buildExclusions(), and NamdState::loadStructure().

char SimParameters::auxFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 211 of file SimParameters.h.

Referenced by CollectionMaster::receiveDataStream().

Bool SimParameters::benchTimestep

Definition at line 167 of file SimParameters.h.

Referenced by Output::coordinateNeeded(), Output::forceNeeded(), and Output::velocityNeeded().

BigReal SimParameters::berendsenPressureCompressibility

Definition at line 684 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

int SimParameters::berendsenPressureFreq

Definition at line 686 of file SimParameters.h.

Referenced by Sequencer::berendsenPressure(), and Controller::berendsenPressure().

Bool SimParameters::berendsenPressureOn

Definition at line 682 of file SimParameters.h.

Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), and ComputeGridForce::doForce().

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 685 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

BigReal SimParameters::berendsenPressureTarget

Definition at line 683 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

Bool SimParameters::binaryOutput

Definition at line 228 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Bool SimParameters::binaryRestart

Definition at line 226 of file SimParameters.h.

char* SimParameters::binAtomFile

Definition at line 1033 of file SimParameters.h.

char* SimParameters::binCoorFile

Definition at line 1034 of file SimParameters.h.

char* SimParameters::binRefFile

Definition at line 1036 of file SimParameters.h.

char* SimParameters::binVelFile

Definition at line 1035 of file SimParameters.h.

int SimParameters::bondedCUDA

Bitmask for calculating bonded interactions on GPU. Default is 255, with the following bit position settings: 1 -> bonds, 2 -> angles, 4 -> dihedrals, 8 -> impropers, 16 -> exclusions, 32 -> crossterms.

Definition at line 803 of file SimParameters.h.

Referenced by ComputeMgr::createComputes(), LdbCoordinator::initialize(), WorkDistrib::mapComputes(), and Node::startup().

zVector SimParameters::cellBasisVector1

Definition at line 127 of file SimParameters.h.

zVector SimParameters::cellBasisVector2

Definition at line 128 of file SimParameters.h.

zVector SimParameters::cellBasisVector3

Definition at line 129 of file SimParameters.h.

zVector SimParameters::cellOrigin

Definition at line 130 of file SimParameters.h.

Bool SimParameters::COLDOn

Definition at line 584 of file SimParameters.h.

BigReal SimParameters::COLDRate

Definition at line 586 of file SimParameters.h.

BigReal SimParameters::COLDTemp

Definition at line 587 of file SimParameters.h.

Bool SimParameters::colvarsOn

Definition at line 561 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), ComputeMgr::createComputes(), Sequencer::integrate(), and Sequencer::minimize().

Bool SimParameters::commOnly

Definition at line 931 of file SimParameters.h.

Referenced by Sequencer::integrate(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces().

Bool SimParameters::comMove

Definition at line 189 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), NamdState::loadStructure(), and Controller::receivePressure().

char SimParameters::computeMapFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 1042 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().

char SimParameters::consForceFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 881 of file SimParameters.h.

Bool SimParameters::consForceOn

Definition at line 880 of file SimParameters.h.

Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

BigReal SimParameters::consForceScaling

Definition at line 882 of file SimParameters.h.

Referenced by ComputeConsForce::doForce().

char SimParameters::consTorqueAxisFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 342 of file SimParameters.h.

char SimParameters::consTorqueFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 340 of file SimParameters.h.

BigReal SimParameters::consTorqueGlobVal

Definition at line 344 of file SimParameters.h.

Referenced by ComputeConsTorque::doForce().

Bool SimParameters::consTorqueOn

Definition at line 339 of file SimParameters.h.

Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::consTorquePivotFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 343 of file SimParameters.h.

char SimParameters::consTorqueValFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 345 of file SimParameters.h.

int SimParameters::constraintExp

Definition at line 263 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

BigReal SimParameters::constraintScaling

Definition at line 291 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

Bool SimParameters::constraintsOn

Definition at line 261 of file SimParameters.h.

Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

Bool SimParameters::constrXOn

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::constrYOn

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::constrZOn

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::cosAngles

Definition at line 550 of file SimParameters.h.

Referenced by Parameters::Parameters().

BigReal SimParameters::coulomb_radius_offset

Definition at line 524 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeGBISser::doWork(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), ComputeNonbondedCUDA::recvYieldDevice(), and HomePatch::setGBISIntrinsicRadii().

BigReal SimParameters::cutoff

Definition at line 230 of file SimParameters.h.

Referenced by GromacsPairElem::computeForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::doMarginCheck(), ComputeQM::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), Sequencer::maximumMove(), Parameters::read_ener_table(), ComputeMsmSerialMgr::recvCoord(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

char SimParameters::cylindricalBCAxis

Definition at line 851 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

int SimParameters::cylindricalBCexp1

Definition at line 856 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

int SimParameters::cylindricalBCexp2

Definition at line 857 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCk1

Definition at line 858 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCk2

Definition at line 859 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCl1

Definition at line 854 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCl2

Definition at line 855 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Bool SimParameters::cylindricalBCOn

Definition at line 848 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::cylindricalBCr1

Definition at line 852 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCr2

Definition at line 853 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

zVector SimParameters::cylindricalCenter

Definition at line 850 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::daCutoffDist

Definition at line 980 of file SimParameters.h.

BigReal SimParameters::daOffDist

Definition at line 980 of file SimParameters.h.

BigReal SimParameters::daOnDist

Definition at line 980 of file SimParameters.h.

char SimParameters::dcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 212 of file SimParameters.h.

int SimParameters::dcdFrequency

Definition at line 202 of file SimParameters.h.

Referenced by Output::coordinate(), and Output::coordinateNeeded().

int SimParameters::dcdUnitCell

Definition at line 204 of file SimParameters.h.

Referenced by Output::coordinate().

BigReal SimParameters::dhaCutoffAngle

Definition at line 976 of file SimParameters.h.

BigReal SimParameters::dhaOffAngle

Definition at line 976 of file SimParameters.h.

BigReal SimParameters::dhaOnAngle

Definition at line 976 of file SimParameters.h.

BigReal SimParameters::dielectric

Definition at line 196 of file SimParameters.h.

Referenced by ComputeMsm::ComputeMsm(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::gbisComputeAfterP2(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

Bool SimParameters::dihedralOn

Definition at line 583 of file SimParameters.h.

Bool SimParameters::disableTopology

Definition at line 164 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

int SimParameters::distAttExp

Definition at line 973 of file SimParameters.h.

int SimParameters::distRepExp

Definition at line 973 of file SimParameters.h.

BigReal SimParameters::drudeBondConst

Definition at line 542 of file SimParameters.h.

Referenced by BondElem::computeForce().

BigReal SimParameters::drudeBondLen

Definition at line 540 of file SimParameters.h.

Referenced by BondElem::computeForce(), HomePatch::hardWallDrude(), and Sequencer::submitMinimizeReductions().

BigReal SimParameters::drudeDamping

Definition at line 538 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::drudeHardWallOn

Definition at line 536 of file SimParameters.h.

Referenced by BondElem::computeForce(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), and Sequencer::submitMinimizeReductions().

BigReal SimParameters::drudeNbtholeCut

Definition at line 543 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::drudeOn

Definition at line 535 of file SimParameters.h.

Referenced by BondElem::computeForce(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Parameters::Parameters(), Controller::printEnergies(), Controller::receivePressure(), Sequencer::reinitVelocities(), ComputeNonbondedUtil::select(), and Sequencer::submitReductions().

BigReal SimParameters::drudeTemp

Definition at line 537 of file SimParameters.h.

Referenced by HomePatch::hardWallDrude(), and Sequencer::langevinVelocitiesBBK2().

BigReal SimParameters::dt

Definition at line 123 of file SimParameters.h.

Referenced by Controller::berendsenPressure(), Controller::Controller(), ComputeEField::doForce(), colvarproxy_namd::dt(), Sequencer::integrate(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::multigratorPressure(), Controller::multigratorTemperature(), Controller::printEnergies(), and ComputeQMMgr::recvPartQM().

zVector SimParameters::eField

Definition at line 863 of file SimParameters.h.

Referenced by ComputeEField::doForce().

BigReal SimParameters::eFieldFreq

Definition at line 864 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Bool SimParameters::eFieldNormalized

Definition at line 862 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Bool SimParameters::eFieldOn

Definition at line 861 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::eFieldPhase

Definition at line 865 of file SimParameters.h.

Referenced by ComputeEField::doForce().

int SimParameters::emptyPatchLoad

Definition at line 949 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

ExclusionSettings SimParameters::exclude

Definition at line 197 of file SimParameters.h.

Referenced by buildExclusions(), and ComputeNonbondedUtil::select().

Bool SimParameters::excludeFromPressure

Definition at line 671 of file SimParameters.h.

Referenced by NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::extCoordFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 461 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

char SimParameters::extForceFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 462 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

char SimParameters::extForcesCommand[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 460 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Bool SimParameters::extForcesOn

Definition at line 459 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::extraBondsCosAngles

Definition at line 877 of file SimParameters.h.

Bool SimParameters::extraBondsCosAnglesSetByUser

Definition at line 878 of file SimParameters.h.

Bool SimParameters::extraBondsOn

Definition at line 876 of file SimParameters.h.

Referenced by Molecule::delete_qm_bonded(), NamdState::loadStructure(), and Molecule::prepare_qm().

Bool SimParameters::FFTWEstimate

Definition at line 817 of file SimParameters.h.

Referenced by PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), and ComputePmeMgr::initialize().

Bool SimParameters::FFTWPatient

Definition at line 818 of file SimParameters.h.

Referenced by PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), and ComputePmeMgr::initialize().

Bool SimParameters::FFTWUseWisdom

Definition at line 819 of file SimParameters.h.

char SimParameters::FFTWWisdomFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 820 of file SimParameters.h.

char* SimParameters::FFTWWisdomString

Definition at line 821 of file SimParameters.h.

int SimParameters::firstLdbStep

Definition at line 141 of file SimParameters.h.

Referenced by LdbCoordinator::initialize(), and Controller::printEnergies().

int SimParameters::firstTimestep

Definition at line 903 of file SimParameters.h.

Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::algorithm(), colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), Output::force(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiming(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Controller::rescaleaccelMD(), Output::velocity(), and Controller::writeFepEnergyData().

Bool SimParameters::fixCellDims

Definition at line 677 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::receivePressure().

Bool SimParameters::fixCellDimX

Definition at line 678 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::receivePressure().

Bool SimParameters::fixCellDimY

Definition at line 679 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::receivePressure().

Bool SimParameters::fixCellDimZ

Definition at line 680 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::receivePressure().

Bool SimParameters::fixedAtomsForceOutput

Definition at line 565 of file SimParameters.h.

Referenced by CollectionMgr::submitForces().

Bool SimParameters::fixedAtomsForces

Definition at line 564 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::positionsReady(), and ComputeNonbondedUtil::select().

Bool SimParameters::fixedAtomsOn

Definition at line 563 of file SimParameters.h.

Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), HomePatch::addVelocityToPosition(), Sequencer::berendsenPressure(), HomePatch::buildRattleList(), Sequencer::calcFixVirial(), Sequencer::correctMomentum(), HomePatch::hardWallDrude(), Sequencer::langevinPiston(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::minimize_rattle2(), Sequencer::minimizeMoveDownhill(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Sequencer::multigratorPressure(), Sequencer::newMinimizeDirection(), HomePatch::positionsReady(), Molecule::prepare_qm(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Controller::receivePressure(), Sequencer::reinitVelocities(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().

int SimParameters::FMAFFTBlock

Definition at line 724 of file SimParameters.h.

Bool SimParameters::FMAFFTOn

Definition at line 723 of file SimParameters.h.

int SimParameters::FMALevels

Definition at line 721 of file SimParameters.h.

int SimParameters::FMAMp

Definition at line 722 of file SimParameters.h.

Bool SimParameters::FMAOn

Definition at line 720 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select().

BigReal SimParameters::fmaTheta

Definition at line 137 of file SimParameters.h.

int SimParameters::FMMLevels

Definition at line 768 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Bool SimParameters::FMMOn

Definition at line 767 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select().

BigReal SimParameters::FMMPadding

Definition at line 769 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

char SimParameters::forceDcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 214 of file SimParameters.h.

int SimParameters::forceDcdFrequency

Definition at line 207 of file SimParameters.h.

Referenced by Output::force(), Output::forceNeeded(), and Output::velocity().

Bool SimParameters::freeEnergyOn

Definition at line 559 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::fsMax

Definition at line 521 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().

Bool SimParameters::fullDirectOn

Definition at line 726 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), and ComputeNonbondedUtil::select().

int SimParameters::fullElectFrequency

Definition at line 135 of file SimParameters.h.

Referenced by Controller::compareChecksums(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects().

BigReal SimParameters::gbis_beta

Definition at line 528 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().

BigReal SimParameters::gbis_delta

Definition at line 527 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().

BigReal SimParameters::gbis_gamma

Definition at line 529 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().

Bool SimParameters::GBISOn

Definition at line 520 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputeCUDAMgr::createCudaComputeNonbonded(), CudaComputeNonbonded::CudaComputeNonbonded(), ComputeNonbondedCUDA::doWork(), CudaComputeNonbonded::doWork(), ComputeNonbondedCUDA::finishReductions(), CudaComputeNonbonded::finishReductions(), ComputeNonbondedCUDA::finishWork(), Sequencer::integrate(), CudaComputeNonbonded::launchWork(), Sequencer::minimize(), ComputeNonbondedCUDA::noWork(), ComputeNonbondedCUDA::recvYieldDevice(), ComputeNonbondedCUDA::registerPatches(), and ComputeNonbondedCUDA::skip().

Bool SimParameters::GBISserOn

Definition at line 522 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes().

Bool SimParameters::genCompressedPsf

Definition at line 1017 of file SimParameters.h.

Referenced by NamdState::configListInit(), and NamdState::loadStructure().

Bool SimParameters::globalForcesOn

Definition at line 551 of file SimParameters.h.

Referenced by ComputeMgr::createComputes(), and WorkDistrib::mapComputes().

Bool SimParameters::globalOn

Definition at line 582 of file SimParameters.h.

char SimParameters::goCoordinates[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 302 of file SimParameters.h.

Bool SimParameters::goForcesOn

Definition at line 300 of file SimParameters.h.

Referenced by NamdState::loadStructure(), Controller::printEnergies(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule().

Bool SimParameters::goGroPair

Definition at line 299 of file SimParameters.h.

Referenced by Controller::compareChecksums(), WorkDistrib::mapComputes(), Controller::printEnergies(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().

GoChoices SimParameters::goMethod

Definition at line 304 of file SimParameters.h.

Referenced by NamdState::loadStructure(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule().

char SimParameters::goParameters[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 301 of file SimParameters.h.

Bool SimParameters::gridforcechecksize

Definition at line 274 of file SimParameters.h.

Bool SimParameters::gridforceContA1

Definition at line 269 of file SimParameters.h.

Bool SimParameters::gridforceContA2

Definition at line 270 of file SimParameters.h.

Bool SimParameters::gridforceContA3

Definition at line 271 of file SimParameters.h.

Bool SimParameters::gridforceLite

Definition at line 273 of file SimParameters.h.

Bool SimParameters::gridforceOn

Definition at line 266 of file SimParameters.h.

zVector SimParameters::gridforceScale

Definition at line 268 of file SimParameters.h.

zVector SimParameters::gridforceVOffset

Definition at line 272 of file SimParameters.h.

Bool SimParameters::gridforceVolts

Definition at line 267 of file SimParameters.h.

Bool SimParameters::gromacsOn

Definition at line 1000 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::haAngleExp

Definition at line 973 of file SimParameters.h.

BigReal SimParameters::hgroupCutoff

Definition at line 915 of file SimParameters.h.

Referenced by HomePatch::doGroupSizeCheck().

int SimParameters::hybridGroupSize

Definition at line 145 of file SimParameters.h.

Referenced by NamdHybridLB::NamdHybridLB().

Bool SimParameters::HydrogenBonds

Definition at line 963 of file SimParameters.h.

Bool SimParameters::ignoreMass

Definition at line 912 of file SimParameters.h.

int SimParameters::IMDfreq

Definition at line 985 of file SimParameters.h.

Referenced by Output::coordinate(), Output::coordinateNeeded(), and Controller::printEnergies().

int SimParameters::IMDignore

Definition at line 988 of file SimParameters.h.

Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDignoreForces

Definition at line 990 of file SimParameters.h.

Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDon

Definition at line 983 of file SimParameters.h.

Referenced by Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), and Controller::printEnergies().

int SimParameters::IMDport

Definition at line 984 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDwait

Definition at line 986 of file SimParameters.h.

Referenced by GlobalMasterIMD::get_vmd_forces(), and GlobalMasterIMD::GlobalMasterIMD().

BigReal SimParameters::initialTemp

Definition at line 187 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Controller::algorithm(), WorkDistrib::createAtomLists(), Sequencer::integrate(), and Sequencer::reinitVelocities().

BigReal SimParameters::ion_concentration

Definition at line 526 of file SimParameters.h.

BigReal SimParameters::kappa

Definition at line 525 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().

Bool SimParameters::langevin_useBAOAB

Definition at line 572 of file SimParameters.h.

Referenced by Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), and Sequencer::langevinVelocitiesBBK2().

BigReal SimParameters::langevinDamping

Definition at line 570 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinHydrogen

Definition at line 571 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinOn

Definition at line 568 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), Molecule::receive_Molecule(), Controller::receivePressure(), and Molecule::send_Molecule().

Bool SimParameters::langevinOnAtStartup

Definition at line 567 of file SimParameters.h.

Bool SimParameters::langevinPistonBarrier

Definition at line 689 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

BigReal SimParameters::langevinPistonDecay

Definition at line 692 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().

Bool SimParameters::langevinPistonOn

Definition at line 688 of file SimParameters.h.

Referenced by ComputeGridForce::doForce(), Sequencer::integrate(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().

BigReal SimParameters::langevinPistonPeriod

Definition at line 691 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().

BigReal SimParameters::langevinPistonTarget

Definition at line 690 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().

BigReal SimParameters::langevinPistonTemp

Definition at line 693 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().

BigReal SimParameters::langevinTemp

Definition at line 569 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2().

int SimParameters::lastLdbStep

Definition at line 143 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

Lattice SimParameters::lattice

Definition at line 131 of file SimParameters.h.

Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), GlobalMasterServer::GlobalMasterServer(), GridforceFullMainGrid::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), Patch::Patch(), WorkDistrib::patchMapInit(), PatchMgr::setLattice(), and Node::startup().

Bool SimParameters::LCPOOn

Definition at line 532 of file SimParameters.h.

Referenced by Sequencer::integrate(), WorkDistrib::mapComputes(), Sequencer::minimize(), Molecule::Molecule(), WorkDistrib::patchMapInit(), Molecule::receive_Molecule(), Molecule::send_Molecule(), NamdHybridLB::splitComputes(), and NamdCentLB::Strategy().

int SimParameters::ldBalancer

Definition at line 138 of file SimParameters.h.

Referenced by LdbCoordinator::createLoadBalancer().

BigReal SimParameters::ldbBackgroundScaling

Definition at line 146 of file SimParameters.h.

BigReal SimParameters::ldbHomeBackgroundScaling

Definition at line 148 of file SimParameters.h.

int SimParameters::ldbPeriod

Definition at line 140 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

BigReal SimParameters::ldbPMEBackgroundScaling

Definition at line 147 of file SimParameters.h.

BigReal SimParameters::ldbRelativeGrainsize

Definition at line 149 of file SimParameters.h.

Referenced by NamdHybridLB::splitComputes(), and NamdCentLB::Strategy().

int SimParameters::ldbStrategy

Definition at line 139 of file SimParameters.h.

Referenced by NamdCentLB::Strategy().

Bool SimParameters::ldbUnloadOne

Definition at line 181 of file SimParameters.h.

Bool SimParameters::ldbUnloadOutputPEs

Definition at line 182 of file SimParameters.h.

Bool SimParameters::ldbUnloadPME

Definition at line 179 of file SimParameters.h.

Bool SimParameters::ldbUnloadZero

Definition at line 180 of file SimParameters.h.

int SimParameters::lesFactor

Definition at line 441 of file SimParameters.h.

Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), Sequencer::reinitVelocities(), ComputePmeUtil::select(), and ComputeNonbondedUtil::select().

Bool SimParameters::lesOn

Definition at line 440 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), ComputePmeCUDA::initialize(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Sequencer::reinitVelocities(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().

Bool SimParameters::lesReduceMass

Definition at line 443 of file SimParameters.h.

Bool SimParameters::lesReduceTemp

Definition at line 442 of file SimParameters.h.

Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().

BigReal SimParameters::limitDist

Definition at line 237 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::LJcorrection

Definition at line 122 of file SimParameters.h.

Referenced by Controller::calcPressure(), NamdState::loadStructure(), Controller::printEnergies(), and Controller::rescaleaccelMD().

Bool SimParameters::loadComputeMap

Definition at line 1044 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::lonepairs

Definition at line 119 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Sequencer::minimize().

int SimParameters::longSplitting

Definition at line 909 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::loweAndersenCutoff

Definition at line 579 of file SimParameters.h.

Bool SimParameters::loweAndersenOn

Definition at line 576 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), and Sequencer::integrate().

BigReal SimParameters::loweAndersenRate

Definition at line 578 of file SimParameters.h.

BigReal SimParameters::loweAndersenTemp

Definition at line 577 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd().

Bool SimParameters::mallocTest

Definition at line 1021 of file SimParameters.h.

Referenced by Node::startup().

BigReal SimParameters::margin

Definition at line 231 of file SimParameters.h.

Referenced by HomePatch::doMarginCheck().

Bool SimParameters::martiniDielAllow

Definition at line 247 of file SimParameters.h.

Bool SimParameters::martiniSwitching

Definition at line 245 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

int SimParameters::maxExclusionFlags

Definition at line 951 of file SimParameters.h.

BigReal SimParameters::maximumMove

Definition at line 833 of file SimParameters.h.

Referenced by Sequencer::maximumMove().

int SimParameters::maxPairPart

Definition at line 937 of file SimParameters.h.

int SimParameters::maxPatches

Definition at line 178 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::maxSelfPart

Definition at line 935 of file SimParameters.h.

Bool SimParameters::mergeCrossterms

Definition at line 901 of file SimParameters.h.

Referenced by Controller::printEnergies().

MGridforceParamsList SimParameters::mgridforcelist

Definition at line 277 of file SimParameters.h.

Referenced by Molecule::build_gridforce_params(), colvarproxy_namd::init_volmap(), Node::reloadGridforceGrid(), and Node::updateGridScale().

Bool SimParameters::mgridforceOn

Definition at line 276 of file SimParameters.h.

Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

int SimParameters::mic_deviceThreshold

Definition at line 1052 of file SimParameters.h.

int SimParameters::mic_hostSplit

Definition at line 1047 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p1

Definition at line 1049 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p2

Definition at line 1050 of file SimParameters.h.

int SimParameters::mic_numParts_self_p1

Definition at line 1048 of file SimParameters.h.

int SimParameters::mic_singleKernel

Definition at line 1053 of file SimParameters.h.

int SimParameters::mic_unloadMICPEs

Definition at line 1051 of file SimParameters.h.

int SimParameters::minAtomsPerPatch

Definition at line 947 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

BigReal SimParameters::minBabyStep

Definition at line 830 of file SimParameters.h.

Bool SimParameters::minimizeCGOn

Definition at line 827 of file SimParameters.h.

Referenced by NamdState::loadStructure(), and ScriptTcl::run().

Bool SimParameters::minimizeOn

Definition at line 832 of file SimParameters.h.

Referenced by Sequencer::minimizationQuenchVelocity().

BigReal SimParameters::minLineGoal

Definition at line 831 of file SimParameters.h.

Referenced by Controller::minimize().

BigReal SimParameters::minTinyStep

Definition at line 829 of file SimParameters.h.

Bool SimParameters::minVerbose

Definition at line 828 of file SimParameters.h.

Referenced by Controller::minimize().

Bool SimParameters::miscForcesOn

Definition at line 560 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

int SimParameters::mollyIter

Definition at line 919 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

int SimParameters::mollyOn

Definition at line 917 of file SimParameters.h.

Referenced by Controller::compareChecksums(), Sequencer::integrate(), and Sequencer::minimize().

BigReal SimParameters::mollyTol

Definition at line 918 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

char SimParameters::movDragFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 322 of file SimParameters.h.

BigReal SimParameters::movDragGlobVel

Definition at line 324 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

Bool SimParameters::movDragOn

Definition at line 321 of file SimParameters.h.

Referenced by Sequencer::integrate(), NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::movDragVelFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 325 of file SimParameters.h.

Bool SimParameters::movingConstraintsOn

Definition at line 308 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

zVector SimParameters::movingConsVel

Definition at line 310 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

int SimParameters::MSMApprox

Definition at line 736 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

int SimParameters::MSMBlockSizeX

Definition at line 746 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

int SimParameters::MSMBlockSizeY

Definition at line 747 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

int SimParameters::MSMBlockSizeZ

Definition at line 748 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMGridSpacing

Definition at line 750 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

int SimParameters::MSMLevels

Definition at line 742 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

Bool SimParameters::MSMOn

Definition at line 729 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), ComputeNonbondedUtil::select(), and Node::startup().

BigReal SimParameters::MSMPadding

Definition at line 752 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

int SimParameters::MSMQuality

Definition at line 732 of file SimParameters.h.

Bool SimParameters::MsmSerialOn

Definition at line 765 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes(), and Node::startup().

int SimParameters::MSMSplit

Definition at line 739 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize(), ComputeMsmSerialMgr::recvCoord(), and ComputeNonbondedUtil::select().

BigReal SimParameters::MSMxmax

Definition at line 759 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMxmin

Definition at line 758 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMymax

Definition at line 761 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMymin

Definition at line 760 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMzmax

Definition at line 763 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMzmin

Definition at line 762 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

MTSChoices SimParameters::MTSAlgorithm

Definition at line 906 of file SimParameters.h.

Referenced by Sequencer::integrate().

int SimParameters::multigratorNoseHooverChainLength

Definition at line 702 of file SimParameters.h.

Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), and Controller::multigratorTemperature().

Bool SimParameters::multigratorOn

Definition at line 695 of file SimParameters.h.

Referenced by Controller::Controller(), LdbCoordinator::initialize(), Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), Controller::multigratorTemperature(), Controller::printEnergies(), Sequencer::Sequencer(), and Sequencer::submitHalfstep().

int SimParameters::multigratorPressureFreq

Definition at line 698 of file SimParameters.h.

Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().

BigReal SimParameters::multigratorPressureRelaxationTime

Definition at line 697 of file SimParameters.h.

Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().

BigReal SimParameters::multigratorPressureTarget

Definition at line 696 of file SimParameters.h.

Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().

int SimParameters::multigratorTemperatureFreq

Definition at line 701 of file SimParameters.h.

Referenced by Sequencer::integrate(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().

BigReal SimParameters::multigratorTemperatureRelaxationTime

Definition at line 700 of file SimParameters.h.

Referenced by Controller::Controller(), and Controller::multigratorTemperature().

BigReal SimParameters::multigratorTemperatureTarget

Definition at line 699 of file SimParameters.h.

Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), Controller::multigratorPressure(), and Controller::multigratorTemperature().

int SimParameters::N

Definition at line 124 of file SimParameters.h.

Referenced by colvarproxy_namd::calculate(), Output::coordinate(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Sequencer::multigratorPressure(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::printEnergies(), Controller::printTiming(), Controller::rescaleaccelMD(), and Output::velocity().

int SimParameters::nonbondedFrequency

Definition at line 133 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::integrate().

BigReal SimParameters::nonbondedScaling

Definition at line 201 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

Bool SimParameters::noPatchesOnOne

Definition at line 185 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnOutputPEs

Definition at line 184 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnZero

Definition at line 183 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::numAtomsPair

Definition at line 943 of file SimParameters.h.

int SimParameters::numAtomsPair2

Definition at line 945 of file SimParameters.h.

int SimParameters::numAtomsSelf

Definition at line 939 of file SimParameters.h.

int SimParameters::numAtomsSelf2

Definition at line 941 of file SimParameters.h.

int SimParameters::numinputprocs

Definition at line 1032 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::numoutputprocs

Definition at line 1039 of file SimParameters.h.

Referenced by NamdState::loadStructure(), and WorkDistrib::patchMapInit().

int SimParameters::numoutputwrts

Definition at line 1040 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::numTraceSteps

Definition at line 152 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::integrate().

Bool SimParameters::oldParmReader

Definition at line 995 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::outputCudaTiming

Definition at line 895 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::finishReductions().

int SimParameters::outputEnergies

Definition at line 884 of file SimParameters.h.

Referenced by Sequencer::integrate(), Controller::printEnergies(), and Controller::printTiming().

int SimParameters::outputEnergiesPrecision

Definition at line 887 of file SimParameters.h.

Referenced by Controller::printEnergies().

char SimParameters::outputFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 216 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::outputExtendedSystem(), and ComputeQMMgr::recvPartQM().

Bool SimParameters::outputMaps

Definition at line 160 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

int SimParameters::outputMomenta

Definition at line 889 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::printEnergies().

int SimParameters::outputPairlists

Definition at line 259 of file SimParameters.h.

Referenced by Controller::compareChecksums(), and Controller::printEnergies().

Bool SimParameters::outputPatchDetails

Definition at line 953 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

int SimParameters::outputPressure

Definition at line 898 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::printEnergies().

int SimParameters::outputTiming

Definition at line 892 of file SimParameters.h.

Referenced by Controller::printTiming().

int SimParameters::pairInteractionGroup1

Definition at line 546 of file SimParameters.h.

int SimParameters::pairInteractionGroup2

Definition at line 547 of file SimParameters.h.

Bool SimParameters::pairInteractionOn

Definition at line 545 of file SimParameters.h.

Referenced by Sequencer::calcKineticEnergy(), WorkDistrib::createAtomLists(), ComputePmeCUDA::initialize(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), Controller::printEnergies(), Molecule::receive_Molecule(), Controller::receivePressure(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

Bool SimParameters::pairInteractionSelf

Definition at line 548 of file SimParameters.h.

Referenced by Sequencer::calcKineticEnergy(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

BigReal SimParameters::pairlistDist

Definition at line 249 of file SimParameters.h.

BigReal SimParameters::pairlistGrow

Definition at line 257 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

int SimParameters::pairlistMinProcs

Definition at line 251 of file SimParameters.h.

BigReal SimParameters::pairlistShrink

Definition at line 256 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

int SimParameters::pairlistsPerCycle

Definition at line 255 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects().

BigReal SimParameters::pairlistTrigger

Definition at line 258 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Bool SimParameters::paraTypeCharmmOn

Definition at line 295 of file SimParameters.h.

Referenced by NamdState::loadStructure(), and Parameters::Parameters().

Bool SimParameters::paraTypeXplorOn

Definition at line 294 of file SimParameters.h.

Referenced by NamdState::loadStructure(), and Parameters::Parameters().

BigReal SimParameters::patchDimension

Definition at line 232 of file SimParameters.h.

Referenced by HomePatch::doMarginCheck(), ComputePmeMgr::initialize(), ComputePmeMgr::initialize_pencils(), and WorkDistrib::patchMapInit().

Bool SimParameters::PMEBarrier

Definition at line 782 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 773 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg(), and ComputeNonbondedUtil::select().

int SimParameters::PMEGridSizeX

Definition at line 775 of file SimParameters.h.

Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

int SimParameters::PMEGridSizeY

Definition at line 776 of file SimParameters.h.

Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

int SimParameters::PMEGridSizeZ

Definition at line 777 of file SimParameters.h.

Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

BigReal SimParameters::PMEGridSpacing

Definition at line 778 of file SimParameters.h.

int SimParameters::PMEInterpOrder

Definition at line 774 of file SimParameters.h.

Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

int SimParameters::PMEMinPoints

Definition at line 781 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEMinSlices

Definition at line 780 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Bool SimParameters::PMEOffload

Definition at line 790 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputePme::ComputePme(), ComputePmeMgr::initialize(), PmePencil< CBase_PmeZPencil >::order_init(), and ComputeNonbondedCUDA::recvYieldDevice().

Bool SimParameters::PMEOn

Definition at line 771 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), WorkDistrib::mapComputes(), Molecule::prepare_qm(), Controller::printEnergies(), ComputeQMMgr::procQMRes(), HomePatch::qmSwapAtoms(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), Node::resendMolecule(), ComputeNonbondedUtil::select(), and Node::startup().

int SimParameters::PMEPencils

Definition at line 783 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEPencilsX

Definition at line 784 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

int SimParameters::PMEPencilsXLayout

Definition at line 788 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEPencilsY

Definition at line 785 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

int SimParameters::PMEPencilsYLayout

Definition at line 787 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEPencilsZ

Definition at line 786 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize(), and ComputePmeCUDAMgr::setupPencils().

int SimParameters::PMEProcessors

Definition at line 779 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMESendOrder

Definition at line 789 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize_pencils().

BigReal SimParameters::PMETolerance

Definition at line 772 of file SimParameters.h.

int SimParameters::pressureProfileAtomTypes

Definition at line 709 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().

Bool SimParameters::pressureProfileEwaldOn

Definition at line 710 of file SimParameters.h.

Referenced by Controller::Controller(), and WorkDistrib::mapComputes().

int SimParameters::pressureProfileEwaldX

Definition at line 711 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldY

Definition at line 712 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldZ

Definition at line 713 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileFreq

Definition at line 708 of file SimParameters.h.

Referenced by Controller::Controller(), and Controller::printEnergies().

Bool SimParameters::pressureProfileOn

Definition at line 706 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), Controller::Controller(), CudaComputeNonbonded::CudaComputeNonbonded(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().

int SimParameters::pressureProfileSlabs

Definition at line 707 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), HomePatch::hardWallDrude(), HomePatch::rattle1old(), ComputeNonbondedUtil::select(), Sequencer::Sequencer(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

Bool SimParameters::printBadContacts

Definition at line 517 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Bool SimParameters::printExclusions

Definition at line 1022 of file SimParameters.h.

int SimParameters::proxyRecvSpanningTree

Definition at line 1026 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

int SimParameters::proxySendSpanningTree

Definition at line 1025 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

int SimParameters::proxyTreeBranchFactor

Definition at line 1028 of file SimParameters.h.

Referenced by Node::startup().

char SimParameters::qmBaseDir[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 475 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmBondColumn[16]

Definition at line 485 of file SimParameters.h.

Bool SimParameters::qmBondDist

Definition at line 486 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmBondOn

Definition at line 484 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmBondScheme

Definition at line 490 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmBondSchemeS[16]

Definition at line 489 of file SimParameters.h.

int SimParameters::qmBondValType

Definition at line 487 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmBondValueTypeS[16]

Definition at line 488 of file SimParameters.h.

Bool SimParameters::qmChrgFromPSF

Definition at line 469 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmChrgMode

Definition at line 473 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmChrgModeS[16]

Definition at line 472 of file SimParameters.h.

char SimParameters::qmColumn[16]

Definition at line 474 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmCSMD

Definition at line 510 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmCSMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 511 of file SimParameters.h.

Bool SimParameters::qmCustomPCSel

Definition at line 502 of file SimParameters.h.

Referenced by ComputeQM::initialize(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().

Bool SimParameters::qmElecEmbed

Definition at line 500 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmEnergyOutFreq

Definition at line 513 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

char SimParameters::qmExecPath[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 470 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmForcesOn

Definition at line 466 of file SimParameters.h.

Referenced by Controller::compareChecksums(), ComputePme::ComputePme(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Controller::printEnergies(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().

int SimParameters::qmFormat

Definition at line 480 of file SimParameters.h.

Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().

int SimParameters::qmLSSFreq

Definition at line 505 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmLSSMode

Definition at line 508 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmLSSModeS[16]

Definition at line 507 of file SimParameters.h.

Bool SimParameters::qmLSSOn

Definition at line 504 of file SimParameters.h.

Referenced by HomePatch::positionsReady(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().

char SimParameters::qmLSSResname[5]

Definition at line 506 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmMOPACAddConfigChrg

Definition at line 482 of file SimParameters.h.

Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmNoPC

Definition at line 499 of file SimParameters.h.

Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().

int SimParameters::qmOutFreq

Definition at line 514 of file SimParameters.h.

Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().

char SimParameters::qmParamPDB[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 467 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::qmParamPDBDefined

Definition at line 468 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::qmPCScheme

Definition at line 495 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSchemeS[16]

Definition at line 494 of file SimParameters.h.

int SimParameters::qmPCSelFreq

Definition at line 501 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmPCSwitchOn

Definition at line 491 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmPCSwitchType

Definition at line 493 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSwitchTypeS[16]

Definition at line 492 of file SimParameters.h.

int SimParameters::qmPosOutFreq

Definition at line 515 of file SimParameters.h.

Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().

char SimParameters::qmPrepProc[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 478 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmPrepProcOn

Definition at line 479 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmReplaceAll

Definition at line 481 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::qmSecProc[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 476 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmSecProcOn

Definition at line 477 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmSimsPerNode

Definition at line 496 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmSoftware[128]

Definition at line 471 of file SimParameters.h.

Bool SimParameters::qmVDW

Definition at line 498 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

unsigned int SimParameters::randomSeed

Definition at line 718 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::Sequencer(), and Node::startup().

Bool SimParameters::readExclusions

Definition at line 996 of file SimParameters.h.

Referenced by buildExclusions().

int SimParameters::reassignFreq

Definition at line 663 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::reassignVelocities(), and Controller::reassignVelocities().

BigReal SimParameters::reassignHold

Definition at line 666 of file SimParameters.h.

Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().

BigReal SimParameters::reassignIncr

Definition at line 665 of file SimParameters.h.

Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().

BigReal SimParameters::reassignTemp

Definition at line 664 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::reassignVelocities(), and Controller::reassignVelocities().

Bool SimParameters::replicaUniformPatchGrids

Definition at line 955 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::rescaleFreq

Definition at line 614 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::rescaleVelocities(), and Controller::rescaleVelocities().

BigReal SimParameters::rescaleTemp

Definition at line 615 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), and Controller::rescaleVelocities().

char SimParameters::restartFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 221 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::outputExtendedSystem().

int SimParameters::restartFrequency

Definition at line 222 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), Controller::outputExtendedSystem(), Controller::rescaleaccelMD(), Output::velocity(), and Output::velocityNeeded().

Bool SimParameters::restartSave

Definition at line 224 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::restartSaveDcd

Definition at line 225 of file SimParameters.h.

int SimParameters::rigidBonds

Definition at line 921 of file SimParameters.h.

Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), outputCompressedFile(), and Sequencer::rattle1().

int SimParameters::rigidDie

Definition at line 926 of file SimParameters.h.

Referenced by HomePatch::hardWallDrude(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().

int SimParameters::rigidIter

Definition at line 925 of file SimParameters.h.

Referenced by HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().

BigReal SimParameters::rigidTol

Definition at line 924 of file SimParameters.h.

Referenced by HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().

zVector SimParameters::rotConsAxis

Definition at line 315 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

zVector SimParameters::rotConsPivot

Definition at line 316 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::rotConstraintsOn

Definition at line 313 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

BigReal SimParameters::rotConsVel

Definition at line 317 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

char SimParameters::rotDragAxisFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 332 of file SimParameters.h.

char SimParameters::rotDragFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 330 of file SimParameters.h.

BigReal SimParameters::rotDragGlobVel

Definition at line 334 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

Bool SimParameters::rotDragOn

Definition at line 329 of file SimParameters.h.

Referenced by Sequencer::integrate(), NamdState::loadStructure(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::rotDragPivotFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 333 of file SimParameters.h.

char SimParameters::rotDragVelFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 335 of file SimParameters.h.

BigReal SimParameters::scale14

Definition at line 199 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::scriptArg1

Definition at line 1006 of file SimParameters.h.

Referenced by Sequencer::algorithm(), Controller::algorithm(), and HomePatch::exchangeAtoms().

BigReal SimParameters::scriptArg2

Definition at line 1007 of file SimParameters.h.

Referenced by HomePatch::exchangeAtoms().

BigReal SimParameters::scriptArg3

Definition at line 1008 of file SimParameters.h.

BigReal SimParameters::scriptArg4

Definition at line 1009 of file SimParameters.h.

BigReal SimParameters::scriptArg5

Definition at line 1010 of file SimParameters.h.

int SimParameters::scriptIntArg1

Definition at line 1011 of file SimParameters.h.

Referenced by Controller::algorithm(), HomePatch::exchangeCheckpoint(), and HomePatch::recvCheckpointLoad().

int SimParameters::scriptIntArg2

Definition at line 1012 of file SimParameters.h.

char SimParameters::scriptStringArg1[128]

Definition at line 1013 of file SimParameters.h.

Referenced by Controller::algorithm(), HomePatch::exchangeCheckpoint(), and HomePatch::recvCheckpointLoad().

char SimParameters::scriptStringArg2[128]

Definition at line 1014 of file SimParameters.h.

Bool SimParameters::sdScaling

Definition at line 392 of file SimParameters.h.

Referenced by NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

Bool SimParameters::selectConstraintsOn

Definition at line 280 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

int SimParameters::simulatedNodeSize

Definition at line 163 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps(), and Node::startup().

int SimParameters::simulatedPEs

Definition at line 162 of file SimParameters.h.

Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().

Bool SimParameters::simulateInitialMapping

Definition at line 161 of file SimParameters.h.

Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().

Bool SimParameters::singleTopology

Definition at line 391 of file SimParameters.h.

Referenced by AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), Sequencer::integrate(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and Sequencer::minimize().

zVector SimParameters::SMDDir

Definition at line 352 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

char SimParameters::SMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 355 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDk

Definition at line 353 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDk2

Definition at line 354 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Bool SimParameters::SMDOn

Definition at line 350 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

int SimParameters::SMDOutputFreq

Definition at line 356 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDVel

Definition at line 351 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Bool SimParameters::soluteScalingAll

enables scaling for bond and angle terms (default is off)

Definition at line 456 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().

BigReal SimParameters::soluteScalingFactor

scaling factor for solute interactions

Definition at line 448 of file SimParameters.h.

Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().

BigReal SimParameters::soluteScalingFactorCharge

optional independent control over scaling factor for electrostatic interactions of solute

Definition at line 450 of file SimParameters.h.

Referenced by Sequencer::algorithm(), and Sequencer::Sequencer().

BigReal SimParameters::soluteScalingFactorVdw

optional independent control over scaling factor for van der Waals interactions of solute

Definition at line 453 of file SimParameters.h.

Bool SimParameters::soluteScalingOn

REST2 (replica exchange solute tempering) on?

Definition at line 446 of file SimParameters.h.

Referenced by LJTable::LJTable(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), and Sequencer::Sequencer().

BigReal SimParameters::solvent_dielectric

Definition at line 523 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().

int SimParameters::sphericalBCexp1

Definition at line 845 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

int SimParameters::sphericalBCexp2

Definition at line 846 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCk1

Definition at line 839 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCk2

Definition at line 841 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Bool SimParameters::sphericalBCOn

Definition at line 836 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::sphericalBCr1

Definition at line 843 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCr2

Definition at line 844 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

zVector SimParameters::sphericalCenter

Definition at line 838 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Bool SimParameters::sphericalConstraintsOn

Definition at line 288 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

zVector SimParameters::sphericalConstrCenter

Definition at line 289 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

int SimParameters::splitPatch

Definition at line 914 of file SimParameters.h.

Bool SimParameters::staticAtomAssignment

Definition at line 954 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), WorkDistrib::patchMapInit(), and HomePatch::positionsReady().

Bool SimParameters::statsOn

Definition at line 932 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::integrate().

int SimParameters::stepsPerCycle

Definition at line 125 of file SimParameters.h.

Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Sequencer::multigratorPressure(), Molecule::prepare_qm(), and Sequencer::runComputeObjects().

zVector SimParameters::stirAxis

Definition at line 873 of file SimParameters.h.

Referenced by ComputeStir::ComputeStir().

char SimParameters::stirFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 868 of file SimParameters.h.

BigReal SimParameters::stirK

Definition at line 872 of file SimParameters.h.

Referenced by ComputeStir::doForce().

Bool SimParameters::stirOn

Definition at line 867 of file SimParameters.h.

Referenced by NamdState::loadStructure(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

zVector SimParameters::stirPivot

Definition at line 874 of file SimParameters.h.

Referenced by ComputeStir::ComputeStir().

BigReal SimParameters::stirStartingTheta

Definition at line 870 of file SimParameters.h.

BigReal SimParameters::stirVel

Definition at line 871 of file SimParameters.h.

int SimParameters::stochRescaleFreq

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 606 of file SimParameters.h.

Referenced by Controller::Controller(), Sequencer::stochRescaleVelocities(), and Controller::stochRescaleVelocities().

Bool SimParameters::stochRescaleHeat

Flag TRUE enables calculation and reporting of heat transfer and work. The computation is cumulative from step = firstTimestep.

Definition at line 609 of file SimParameters.h.

Referenced by Controller::printEnergies().

Bool SimParameters::stochRescaleOn

Flag TRUE enables the stochastic velocity rescaling method of Bussi, Donadio, and Parrinello. The method is an extension to the Berendsen thermostat, where a stochastic update to the velocity rescaling produces correct sampling of the NVT ensemble.

Definition at line 593 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Controller::printEnergies(), Sequencer::stochRescaleVelocities(), and Controller::stochRescaleVelocities().

BigReal SimParameters::stochRescalePeriod

Timescale (ps) for stochastic velocity rescaling.

Definition at line 603 of file SimParameters.h.

Referenced by Controller::Controller().

BigReal SimParameters::stochRescaleTemp

Temperature for stochastic velocity rescaling.

Definition at line 600 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::stochRescaleCoefficient().

Bool SimParameters::storeComputeMap

Definition at line 1043 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().

zVector SimParameters::strainRate

Definition at line 715 of file SimParameters.h.

Referenced by Controller::Controller().

zVector SimParameters::strainRate2

Definition at line 716 of file SimParameters.h.

Referenced by Controller::Controller().

BigReal SimParameters::surface_tension

Definition at line 533 of file SimParameters.h.

Referenced by ComputeLCPO::ComputeLCPO().

BigReal SimParameters::surfaceTensionTarget

Definition at line 704 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().

Bool SimParameters::switchingActive

Definition at line 239 of file SimParameters.h.

Referenced by ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

BigReal SimParameters::switchingDist

Definition at line 243 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

char SimParameters::symmetryFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 380 of file SimParameters.h.

int SimParameters::symmetryFirstFullStep

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryFirstStep

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

BigReal SimParameters::symmetryk

Definition at line 378 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetrykfile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 379 of file SimParameters.h.

int SimParameters::symmetryLastFullStep

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryLastStep

Definition at line 382 of file SimParameters.h.

Referenced by ComputeMgr::createComputes(), and GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetryMatrixFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 381 of file SimParameters.h.

Bool SimParameters::symmetryOn

Definition at line 377 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Bool SimParameters::symmetryScaleForces

Definition at line 377 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::tableInterpType[128]

Definition at line 363 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

BigReal SimParameters::tableMaxDist

Definition at line 365 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

int SimParameters::tableNumTypes

Definition at line 361 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Real SimParameters::tableSpacing

Definition at line 364 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Bool SimParameters::tabulatedEnergies

Definition at line 360 of file SimParameters.h.

Referenced by Parameters::Parameters(), and ComputeNonbondedUtil::select().

char SimParameters::tabulatedEnergiesFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 362 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

char SimParameters::tclBCArgs[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 558 of file SimParameters.h.

Referenced by ComputeTclBC::doWork().

Bool SimParameters::tclBCOn

Definition at line 556 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

char* SimParameters::tclBCScript

Definition at line 557 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Bool SimParameters::tclForcesOn

Definition at line 552 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), ComputeMgr::createComputes(), Sequencer::integrate(), and Sequencer::minimize().

Bool SimParameters::tclIsThreaded

Definition at line 554 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Bool SimParameters::tCoupleOn

Definition at line 589 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), NamdState::loadStructure(), Molecule::receive_Molecule(), Molecule::send_Molecule(), Sequencer::tcoupleVelocities(), and Controller::tcoupleVelocities().

BigReal SimParameters::tCoupleTemp

Definition at line 591 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::tcoupleVelocities().

Bool SimParameters::testOn

Definition at line 930 of file SimParameters.h.

Bool SimParameters::TMDDiffRMSD

Definition at line 369 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile2[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDFinalRMSD

Definition at line 374 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDFirstStep

Definition at line 373 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDInitialRMSD

Definition at line 374 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDk

Definition at line 370 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDLastStep

Definition at line 373 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Bool SimParameters::TMDOn

Definition at line 369 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

int SimParameters::TMDOutputFreq

Definition at line 372 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::totalAtoms

Definition at line 934 of file SimParameters.h.

int SimParameters::traceStartStep

Definition at line 151 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::integrate().

int SimParameters::twoAwayX

Definition at line 175 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayY

Definition at line 176 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayZ

Definition at line 177 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::useAntecedent

Definition at line 966 of file SimParameters.h.

Bool SimParameters::useAVXTiles

Definition at line 1056 of file SimParameters.h.

Referenced by Patch::positionsReady(), HomePatch::positionsReady(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), and ComputeNonbondedUtil::select().

int SimParameters::useCkLoop

Definition at line 173 of file SimParameters.h.

Referenced by PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), PmeZPencil::fft_init(), PmeXPencil::fft_init(), PmeZPencil::forward_fft(), PmeYPencil::forward_fft(), PmeXPencil::forward_fft(), ComputePmeCUDADevice::gatherForceDone(), PmeZPencil::send_all_ungrid(), PmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), and Node::startup().

Bool SimParameters::useCompressedPsf

Definition at line 1016 of file SimParameters.h.

Referenced by NamdState::loadStructure(), and Molecule::Molecule().

Bool SimParameters::useConstantArea

Definition at line 674 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

Bool SimParameters::useConstantRatio

Definition at line 675 of file SimParameters.h.

Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), and Controller::langevinPiston2().

Bool SimParameters::useCUDA2

Flag TRUE to use the second generation nonbonded CUDA kernels developed by Antti-Pekka Hynninen. Default is TRUE.

Definition at line 798 of file SimParameters.h.

Referenced by ComputePmeMgr::chargeGridSubmitted(), ComputeMgr::createComputes(), WorkDistrib::mapComputes(), ComputeNonbondedUtil::select(), and Node::startup().

Bool SimParameters::useCUDAdisable

Flag TRUE to automatically disable individual CUDA kernels that are incompatible with simulation options. Default is TRUE. Specifically, disable CUDA bonds for Drude oscillator simulation and disable CUDA dihedral and CUDA crossterms kernels for accelMDdihe and accelMDdual simulation. Set FALSE to manually control kernel use for development.

Definition at line 809 of file SimParameters.h.

Bool SimParameters::useDPME

Definition at line 792 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::useFlexibleCell

Definition at line 673 of file SimParameters.h.

Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), and Controller::langevinPiston2().

Bool SimParameters::useGroupPressure

Definition at line 668 of file SimParameters.h.

Referenced by Sequencer::berendsenPressure(), Controller::calcPressure(), Sequencer::langevinPiston(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Controller::receivePressure(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

int SimParameters::usePairlists

Definition at line 253 of file SimParameters.h.

Bool SimParameters::usePluginIO

Definition at line 1019 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::usePMECUDA

Flag TRUE to use the PME CUDA version. Default is TRUE if running on 4 nodes or less.

Definition at line 794 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA(), isPmeProcessor(), WorkDistrib::mapComputes(), ComputeNonbondedCUDA::recvYieldDevice(), and Node::startup().

Bool SimParameters::useSettle

Definition at line 928 of file SimParameters.h.

Referenced by HomePatch::buildRattleList(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().

Bool SimParameters::vdwForceSwitching

Definition at line 241 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::vdwGeometricSigma

Definition at line 1003 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::vdwscale14

Definition at line 997 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::velDcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 213 of file SimParameters.h.

int SimParameters::velDcdFrequency

Definition at line 205 of file SimParameters.h.

Referenced by Output::velocity(), and Output::velocityNeeded().

Bool SimParameters::verboseTopology

Definition at line 165 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

int SimParameters::watmodel

Definition at line 120 of file SimParameters.h.

Referenced by HomePatch::buildRattleList(), HomePatch::minimize_rattle2(), HomePatch::rattle1(), HomePatch::rattle1old(), and HomePatch::rattle2().

Bool SimParameters::wrapAll

Definition at line 194 of file SimParameters.h.

Referenced by colvarproxy_namd::setup(), and wrap_coor_int().

Bool SimParameters::wrapNearest

Definition at line 195 of file SimParameters.h.

Referenced by wrap_coor_int().

Bool SimParameters::wrapWater

Definition at line 193 of file SimParameters.h.

Referenced by wrap_coor_int().

char SimParameters::xstFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 215 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

int SimParameters::xstFrequency

Definition at line 209 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::zeroMomentum

Definition at line 191 of file SimParameters.h.

Referenced by Sequencer::integrate(), and Controller::integrate().

Bool SimParameters::zeroMomentumAlt

Definition at line 192 of file SimParameters.h.

Referenced by Sequencer::correctMomentum(), and Sequencer::submitMomentum().

The documentation for this class was generated from the following files:
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