#include <SimParameters.h>

Public Member Functions
BigReal	getCurrentLambda (const int) const

BigReal	getCurrentLambda2 (const int) const

int	setupIDWS ()

BigReal	getLambdaDelta (void) const

BigReal	getElecLambda (const BigReal) const

BigReal	getVdwLambda (const BigReal) const

BigReal	getRepLambda (const BigReal) const

BigReal	getBondLambda (const BigReal) const

size_t	alchGetNumOfPMEGrids () const

	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 ()

bool	isMultiTimeStepping ()

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
int	mshakeOn

int	lincsOn

Bool	SOAintegrateOn

Bool	CUDASOAintegrateMode

Bool	GPUresidentMode

Bool	CUDASOAintegrate

int	movingAverageWindowSize

Bool	nsPerDayOn

Bool	lonepairs

WaterModel	watmodel

Bool	LJcorrection

Bool	LJcorrectionAlt

BigReal	dt

int	N

int	stepsPerCycle

zVector	cellBasisVector1

zVector	cellBasisVector2

zVector	cellBasisVector3

zVector	cellOrigin

Lattice	lattice

int	nonbondedFrequency

int	fullElectFrequency

int	fullDispersionFrequency

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	scale14alt

BigReal	nonbondedScaling

int	dcdFrequency

int	dcdUnitCell

int	velDcdFrequency

int	forceDcdFrequency

int	xstFrequency

int	dcdSelectionOn

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	groupRestraintsOn

GroupRestraintList	groupRestraints

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	qmBondColumnDefined

Bool	qmBondDist

Bool	qmBondGuess

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

int	globalMasterFrequency

Bool	globalMasterScaleByFrequency

Bool	globalMasterStaleForces

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	langevinGammasDiffer

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	monteCarloPressureOnAtStartup

Bool	monteCarloPressureOn

BigReal	monteCarloPressureTarget

BigReal	monteCarloTemp

BigReal	monteCarloAcceptanceRate

zVector	monteCarloMaxVolume

int	monteCarloAdjustmentFreq

int	monteCarloPressureFreq

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	LJPMEOn

BigReal	LJPMETolerance

BigReal	LJPMEEwaldCoefficient

int	LJPMEInterpOrder

int	LJPMEGridSizeX

int	LJPMEGridSizeY

int	LJPMEGridSizeZ

BigReal	LJPMEGridSpacing

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	usePMEGPU

int	bondedCUDA

int	bondedGPU

Bool	useCUDAdisable

Bool	useCUDANonbondedForceTable

Bool	useGPUNonbondedForceTable

Bool	useDeviceMigration

Bool	useGPUAtomMigration

Bool	updateAtomMap

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	computeEnergies

int	outputEnergies

int	outputEnergiesPrecision

int	outputMomenta

int	outputTiming

Bool	outputPerformance

int	benchmarkTime

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

Bool	useCudaGlobal

int	cudaGlobalProfilingFreq

Bool	usePytorchForces

Detailed Description

Definition at line 102 of file SimParameters.h.

Constructor & Destructor Documentation

◆ SimParameters() [1/2]

SimParameters::SimParameters ( )

inline

Definition at line 1154 of file SimParameters.h.

1154 : mgridforcelist(), parseopts(0) {};

SimParameters::mgridforcelist

MGridforceParamsList mgridforcelist

Definition: SimParameters.h:311

◆ SimParameters() [2/2]

SimParameters::SimParameters	(	ConfigList *	c,
		char *&	cwd
	)

inline

Definition at line 1155 of file SimParameters.h.

References initialize_config_data().

                                                  : mgridforcelist(), parseopts(0) {
           initialize_config_data(c,cwd);
         };

◆ ~SimParameters()

SimParameters::~SimParameters ( )

inline

Definition at line 1158 of file SimParameters.h.

1158 {};

Member Function Documentation

◆ alchGetNumOfPMEGrids()

size_t SimParameters::alchGetNumOfPMEGrids ( ) const

Definition at line 8434 of file SimParameters.C.

Referenced by CudaPmeOneDevice::CudaPmeOneDevice().

                                                  {
   size_t num_max_grids = 1;
   if (!alchOn) return num_max_grids;
   if (alchFepOn && !alchThermIntOn) {
     num_max_grids += 1;
     if (alchDecouple) {
       num_max_grids += 2;
     }
     if (alchElecLambdaStart > 0) {
       num_max_grids += 1;
     }
   }
   if (!alchFepOn && alchThermIntOn) {
     num_max_grids += 2;
     if (alchDecouple) {
       num_max_grids += 2;
     }
   }
   return num_max_grids;
     
 }

◆ close_dcdfile()

void SimParameters::close_dcdfile ( )

Definition at line 813 of file Output.C.

References Molecule::dcdSelectionParams, END_OF_RUN, dcd_params::frequency, Node::molecule, Node::Object(), Node::output, and dcd_params::tag.

                                   {
 
   Output *output = Node::Object()->output;
   if ( ! output ) return;
 
   output->output_dcdfile(END_OF_RUN, 0, 0, 0, 0);
   Molecule *molecule = Node::Object()->molecule;
   for(int dcdSelectionIndex=0; dcdSelectionIndex<16;++dcdSelectionIndex)
     {
       int dcdSelectionFrequency = molecule->dcdSelectionParams[dcdSelectionIndex].frequency;
       int dcdSelectionTag = molecule->dcdSelectionParams[dcdSelectionIndex].tag;
       if(dcdSelectionFrequency)
         output->output_dcdfile(END_OF_RUN,0,0,0,dcdSelectionTag);
     }
 }

◆ close_veldcdfile()

void SimParameters::close_veldcdfile ( )

Definition at line 829 of file Output.C.

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

                                      {
 
   Output *output = Node::Object()->output;
   if ( ! output ) return;
 
   output->output_veldcdfile(END_OF_RUN, 0, 0);
 
 }

◆ getBondLambda()

BigReal SimParameters::getBondLambda ( const BigReal lambda ) const

Definition at line 8429 of file SimParameters.C.

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

                                                                {
   // Convenience function for staggered lambda scaling
   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
 }

◆ getCurrentLambda()

BigReal SimParameters::getCurrentLambda ( const int step ) const

Definition at line 8350 of file SimParameters.C.

Referenced by Controller::calcPressure(), Controller::computeAlchWork(), Controller::getTotalPotentialEnergy(), and Controller::printEnergies().

                                                             {
   /*Get lambda at the current step. 
 
    If alchLambdaFreq = 0, return alchLambda. For positive values of 
    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
    alchLambda2:
 
    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
 
    n - the current time step
    n0 - step at which switching begins (default = 0)
    N - total steps in the simulation
    dn - alchLambdaFreq (increment frequency, in steps)
    l/l2 - alchLambda/alchLambda2
  
    Note that each step _begins_ by incrementing alchLambda and then integrates
    in time. This means that the first and last switch steps may not behave as
    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
    no step occurs because alchLambda2 has already been reached.
   */
   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
     if ( step == N ) {
       return alchLambda2;
     }
     else {
       const int timeOrigin = firstTimestep + alchEquilSteps;
       const BigReal alchLambdaDelta = getLambdaDelta();
       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
     }
   }
   else {
     return alchLambda;
   }
 }

◆ getCurrentLambda2()

BigReal SimParameters::getCurrentLambda2 ( const int step ) const

Definition at line 8300 of file SimParameters.C.

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

                                                              {
   if ( alchLambdaIDWS >= 0. ) {
     const BigReal lambda2 = ( (step / alchIDWSFreq) % 2 == 1 ) ? alchLambda2 : alchLambdaIDWS;
     return lambda2;
   } else {
     return alchLambda2;
   }
 }

◆ getElecLambda()

BigReal SimParameters::getElecLambda ( const BigReal lambda ) const

Definition at line 8392 of file SimParameters.C.

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

                                                                {
   // Convenience function for staggered lambda scaling
   return (lambda <= alchElecLambdaStart ? 0.
           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
 }

◆ getfromparseopts()

char * SimParameters::getfromparseopts	(	const char *	name,
		char *	outbuf
	)

Definition at line 107 of file SimParameters.C.

                                                                     {
   if ( parseopts ) return parseopts->getfromptr(name,outbuf);
   else return 0;
 }

◆ getLambdaDelta()

BigReal SimParameters::getLambdaDelta ( void ) const

Definition at line 8386 of file SimParameters.C.

Referenced by Controller::outputTiEnergy().

                                                 {
   // Increment by which Lambda changes.
   return ((alchLambda2 - alchLambda)*alchLambdaFreq
           / BigReal(N - firstTimestep - alchEquilSteps));
 }

◆ getRepLambda()

BigReal SimParameters::getRepLambda ( const BigReal lambda ) const

Definition at line 8424 of file SimParameters.C.

                                                               {
   // Convenience function for staggered lambda scaling
   return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd);
 }

◆ getVdwLambda()

BigReal SimParameters::getVdwLambda ( const BigReal lambda ) const

Definition at line 8406 of file SimParameters.C.

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

                                                               {
   // Convenience function for staggered lambda scaling
   if ( alchWCAOn ) {
     // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart.
     // The second condition is needed when attractive interactions are inactive
     // for the whole range, otherwise lambda = 0/1 are incorrect.
     if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) {
       return 0.0;
     } else if ( lambda >= alchVdwLambdaEnd ) {
       return 1.0;
     } else {
       return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd);
     }
   } else {
     return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
   }
 }

◆ initialize_config_data()

void SimParameters::initialize_config_data	(	ConfigList *	config,
		char *&	cwd
	)

Definition at line 135 of file SimParameters.C.

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

Referenced by SimParameters().

 {
 
    parseopts = new ParseOptions;   //  Object to check consistency of config file
    ParseOptions &opts = *parseopts;
 
    config_parser(opts);
 
    if (!opts.check_consistency()) 
    {
       NAMD_die("Internal error in configuration file parser");
    }
 
    // Now, feed the object with the actual configuration options through the
    // ParseOptions file and make sure everything is OK
    if (!opts.set(*config)) 
    {
       NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
    }
 
 
    check_config(opts,config,cwd);
 
    print_config(opts,config,cwd);
 
 }

◆ isMultiTimeStepping()

bool SimParameters::isMultiTimeStepping ( )

inline

Definition at line 1183 of file SimParameters.h.

References fullElectFrequency, and nonbondedFrequency.

Referenced by Controller::calcPressure().

                                    {
           return (fullElectFrequency != 1) || (nonbondedFrequency != 1);
         }

◆ isRecvSpanningTreeOn()

int SimParameters::isRecvSpanningTreeOn ( )

inline

Definition at line 1180 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

1180 { return proxyRecvSpanningTree == 1; }

SimParameters::proxyRecvSpanningTree

int proxyRecvSpanningTree

Definition: SimParameters.h:1115

◆ isRecvSpanningTreeUnset()

int SimParameters::isRecvSpanningTreeUnset ( )

inline

Definition at line 1181 of file SimParameters.h.

References proxyRecvSpanningTree.

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

1181 { return proxyRecvSpanningTree == -1; }

SimParameters::proxyRecvSpanningTree

int proxyRecvSpanningTree

Definition: SimParameters.h:1115

◆ isSendSpanningTreeOn()

int SimParameters::isSendSpanningTreeOn ( )

inline

Definition at line 1178 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

1178 { return proxySendSpanningTree == 1; }

SimParameters::proxySendSpanningTree

int proxySendSpanningTree

Definition: SimParameters.h:1114

◆ isSendSpanningTreeUnset()

int SimParameters::isSendSpanningTreeUnset ( )

inline

Definition at line 1179 of file SimParameters.h.

References proxySendSpanningTree.

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

1179 { return proxySendSpanningTree == -1; }

SimParameters::proxySendSpanningTree

int proxySendSpanningTree

Definition: SimParameters.h:1114

◆ issetinparseopts()

int SimParameters::issetinparseopts ( const char * name )

Definition at line 117 of file SimParameters.C.

                                                     {
   if ( parseopts ) return parseopts->issetfromptr(name);
   else return -1;
 }

◆ istrueinparseopts()

int SimParameters::istrueinparseopts ( const char * name )

Definition at line 112 of file SimParameters.C.

                                                      {
   if ( parseopts ) return parseopts->istruefromptr(name);
   else return -1;
 }

◆ nonbonded_select()

void SimParameters::nonbonded_select ( )

static

Definition at line 473 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

                                      {
     ComputeNonbondedUtil::select();
 }

◆ pme_select()

void SimParameters::pme_select ( )

static

Definition at line 477 of file SimParameters.C.

References ComputePmeUtil::select().

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

                                {
   ComputePmeUtil::select();
 }

◆ readExtendedSystem()

void SimParameters::readExtendedSystem	(	const char *	filename,
		Lattice *	latptr = `0`
	)

Definition at line 2585 of file SimParameters.C.

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

                                                                             {
 
      if ( ! latptr ) {
        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
      }
 
      ifstream xscFile(filename);
      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
 
      char labels[1024];
      do {
        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
        xscFile.getline(labels,1023);
      } while ( strncmp(labels,"#$LABELS ",9) );
 
      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
      int v_x = -1, v_y = -1 , v_z = -1;
 
      int pos = 0;
      char *l_i = labels + 8;
      while ( *l_i ) {
        if ( *l_i == ' ' ) { ++l_i; continue; }
        char *l_i2;
        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
          if (l_i[0] == 'v' && l_i[2] == 'x') v_x = pos;
          if (l_i[0] == 'v' && l_i[2] == 'y') v_y = pos;
          if (l_i[0] == 'v' && l_i[2] == 'z') v_z = pos;
        }
        ++pos;
        l_i = l_i2;
      }
      int numpos = pos;
 
      for ( pos = 0; pos < numpos; ++pos ) {
        double tmp;
        xscFile >> tmp;
        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
        if ( pos == a_x ) cellBasisVector1.x = tmp;
        if ( pos == a_y ) cellBasisVector1.y = tmp;
        if ( pos == a_z ) cellBasisVector1.z = tmp;
        if ( pos == b_x ) cellBasisVector2.x = tmp;
        if ( pos == b_y ) cellBasisVector2.y = tmp;
        if ( pos == b_z ) cellBasisVector2.z = tmp;
        if ( pos == c_x ) cellBasisVector3.x = tmp;
        if ( pos == c_y ) cellBasisVector3.y = tmp;
        if ( pos == c_z ) cellBasisVector3.z = tmp;
        if ( pos == o_x ) cellOrigin.x = tmp;
        if ( pos == o_y ) cellOrigin.y = tmp;
        if ( pos == o_z ) cellOrigin.z = tmp;
        if ( pos == s_u ) strainRate2.x = tmp;
        if ( pos == s_v ) strainRate2.y = tmp;
        if ( pos == s_w ) strainRate2.z = tmp;
        if ( pos == s_x ) strainRate.x = tmp;
        if ( pos == s_y ) strainRate.y = tmp;
        if ( pos == s_z ) strainRate.z = tmp;
        if ( pos == v_x ) monteCarloMaxVolume.x = tmp;
        if ( pos == v_y ) monteCarloMaxVolume.y = tmp;
        if ( pos == v_z ) monteCarloMaxVolume.z = tmp;
      }
 
    if ( latptr ) {
      Lattice test;
      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
     
      if ( test.a_p() && ! lattice.a_p() ) {
        NAMD_die("cellBasisVector1 added during atom reinitialization");
      }
      if ( lattice.a_p() && ! test.a_p() ) {
        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
      }
      if ( test.b_p() && ! lattice.b_p() ) {
        NAMD_die("cellBasisVector2 added during atom reinitialization");
      }
      if ( lattice.b_p() && ! test.b_p() ) {
        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
      }
      if ( test.c_p() && ! lattice.c_p() ) {
        NAMD_die("cellBasisVector3 added during atom reinitialization");
      }
      if ( lattice.c_p() && ! test.c_p() ) {
        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
      }
 
      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
    }
 
 }

◆ receive_SimParameters()

void SimParameters::receive_SimParameters ( MIStream * msg )

Definition at line 8241 of file SimParameters.C.

References MIStream::get().

 {
   msg->get(sizeof(SimParameters),(char*)this);
   if ( FFTWWisdomString ) {
     int fftwlen;
     msg->get(fftwlen);
     FFTWWisdomString = new char[fftwlen];
     msg->get(fftwlen,FFTWWisdomString);
 #ifdef NAMD_FFTW
 #ifdef NAMD_FFTW_3
     fftwf_import_wisdom_from_string(FFTWWisdomString);
 #else
     fftw_import_wisdom_from_string(FFTWWisdomString);
 #endif
 #endif
   }
   if ( tclBCScript ) {
     int tcllen;
     msg->get(tcllen);
     tclBCScript = new char[tcllen];
     msg->get(tcllen,tclBCScript);
   }
 
 #ifdef MEM_OPT_VERSION
   int filelen;
   msg->get(filelen);
   binAtomFile = new char[filelen];
   msg->get(filelen, binAtomFile);
   
   msg->get(filelen);
   binCoorFile = new char[filelen];
   msg->get(filelen, binCoorFile);
 
   if(binVelFile) {    
     msg->get(filelen);
     binVelFile = new char[filelen];
     msg->get(filelen, binVelFile);
   }
 
   if(binRefFile) {    
     msg->get(filelen);
     binRefFile = new char[filelen];
     msg->get(filelen, binRefFile);
   }
 #endif
 
 
   // The simParameters bit copy above put illegal values in the list pointers
   // So this resets everything so that unpacking will work.
   mgridforcelist.clear();
   mgridforcelist.unpack_data(msg);
   
   delete msg;
 }

◆ scriptSet()

void SimParameters::scriptSet	(	const char *	param,
		const char *	value
	)

Definition at line 177 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().

                                                                   {
 
   if ( CkMyRank() ) return;
 
 #define MAX_SCRIPT_PARAM_SIZE 128
 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
 
   SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
   SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
   SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
   SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
   SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
   SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1)
   SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2)
   SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1)
   SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2)
   SCRIPT_PARSE_INT("numsteps",N)
   if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) {
     N = firstTimestep = atoi(value); return;
   }
   SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
   SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
   SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
   SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
   // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
   if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) {
     langevinOn = atobool(value);
     if ( langevinOn && ! langevinOnAtStartup ) {
       NAMD_die("Langevin must be enabled at startup to disable and re-enable in script.");
     }
     return;
   }
   SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
   SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
   SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
   SCRIPT_PARSE_BOOL("stochRescale",stochRescaleOn)
   SCRIPT_PARSE_FLOAT("stochRescaleTemp",stochRescaleTemp)
   SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
   SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
   SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
   SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
   SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
   SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
   SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
   SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
   SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
   SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
   SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
                         langevinPistonTarget,/PRESSUREFACTOR)
   SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
   SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
   SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
   SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
                         surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
   SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
                         berendsenPressureTarget,/PRESSUREFACTOR)
   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
                         berendsenPressureCompressibility,*PRESSUREFACTOR)
   SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
                                 berendsenPressureRelaxationTime)
   //MC pressure control
   if ( ! strncasecmp(param,"monteCarloPressureOn",MAX_SCRIPT_PARAM_SIZE) ) {
     monteCarloPressureOn = atobool(value);
     if ( monteCarloPressureOn && ! monteCarloPressureOnAtStartup ) {
       NAMD_die("Monte Carlo pressure control must be enabled at startup to disable and re-enable in script.");
     }
     return;
   }
   SCRIPT_PARSE_MOD_FLOAT("monteCarloPressureTarget",
                         monteCarloPressureTarget,/PRESSUREFACTOR)
   SCRIPT_PARSE_FLOAT("monteCarloTemp",monteCarloTemp)
   SCRIPT_PARSE_FLOAT("monteCarloAcceptanceRate",monteCarloAcceptanceRate)
   SCRIPT_PARSE_INT("monteCarloPressureFreq",monteCarloPressureFreq)
   SCRIPT_PARSE_INT("monteCarloAdjustmentFreq",monteCarloAdjustmentFreq)
   //
   SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
   SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
   SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn)
   SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst)
   SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen)
   SCRIPT_PARSE_STRING("outputname",outputFilename)
   SCRIPT_PARSE_INT("computeEnergies", computeEnergies)
   SCRIPT_PARSE_INT("outputEnergies",outputEnergies)
   SCRIPT_PARSE_INT("outputEnergiesPrecision",outputEnergiesPrecision)
   SCRIPT_PARSE_STRING("restartname",restartFilename)
   SCRIPT_PARSE_INT("DCDfreq",dcdFrequency)
   if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
     close_dcdfile();  // *** implemented in Output.C ***
     strcpy(dcdFilename,value);
     return;
   }
   if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
     close_veldcdfile();  // *** implemented in Output.C ***
     strcpy(velDcdFilename,value);
     return;
   }
   SCRIPT_PARSE_INT("globalMasterFrequency",globalMasterFrequency)
   SCRIPT_PARSE_BOOL("globalMasterScaleByFrequency",globalMasterScaleByFrequency)
   SCRIPT_PARSE_BOOL("globalMasterStaleForces",globalMasterStaleForces)
   SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
   SCRIPT_PARSE_VECTOR("eField",eField)
   SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
   SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
   SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 
   SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 
   SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 
   SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 
   SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 
   SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 
   SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile)
   SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
   SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
 
   if ( ! strncasecmp(param,"CUDASOAintegrate",MAX_SCRIPT_PARAM_SIZE) || 
        ! strncasecmp(param,"GPUresident",MAX_SCRIPT_PARAM_SIZE) ) {
     if ( ! CUDASOAintegrateMode ) {
       NAMD_die("Can't modify CUDASOAintegrate when that mode was never enabled");
     }
     CUDASOAintegrate = atobool(value);
     return;
   }
 
   if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
     NAMD_die("Can't yet modify mgridforcescale in a script");
     return;
   }
   if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
     NAMD_die("Can't yet modify mgridforcevoff in a script");
     return;
   }
    
   if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
     if ( ! fixedAtomsOn )
       NAMD_die("FixedAtoms may not be enabled in a script.");
     if ( ! fixedAtomsForces )
       NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
     fixedAtomsOn = atobool(value);
     return;
   }
 
 //fepb
   if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) {
     alchOn = atobool(value);
     if ( alchOn && ! alchOnAtStartup ) {
        NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script.");
     }
     alchFepOn = alchOn && alchFepOnAtStartup;
     alchThermIntOn = alchOn && alchThermIntOnAtStartup;
     ComputeNonbondedUtil::select();
     if ( PMEOn ) ComputePmeUtil::select();
 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
 #ifdef BONDED_CUDA
     if (bondedCUDA > 0) {
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchFlags();
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchFlags();
     }
 #endif // BONDED_CUDA
 #endif // NAMD_CUDA
     return;
   }
   SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
 
   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
     alchLambda = atof(value);
     if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
     }
     ComputeNonbondedUtil::select();
 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
 #ifdef BONDED_CUDA
     if (bondedCUDA > 0) {
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
     }
 #endif // BONDED_CUDA
 #endif // NAMD_CUDA
     return;
   }
 
   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
     alchLambda2 = atof(value);
     if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
     }
     ComputeNonbondedUtil::select();
 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
 #ifdef BONDED_CUDA
     if (bondedCUDA > 0) {
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
     }
 #endif // BONDED_CUDA
 #endif // NAMD_CUDA
     return;
   }
 
   if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
     alchLambdaIDWS = atof(value);
     setupIDWS();
     ComputeNonbondedUtil::select();
 #ifdef NAMD_CUDA
 #ifdef BONDED_CUDA
     if (bondedCUDA > 0) {
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
     }
 #endif // BONDED_CUDA
 #endif // NAMD_CUDA
     return;
   }
 
   if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
     alchLambdaFreq = atoi(value);
     if ( alchLambdaIDWS >= 0 ) {
       NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n");
     }
     ComputeNonbondedUtil::select();
 #ifdef NAMD_CUDA
 #ifdef BONDED_CUDA
     if (bondedCUDA > 0) {
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateHostCudaAlchLambdas();
       ComputeCUDAMgr::getComputeCUDAMgr()->getComputeBondedCUDA()->updateKernelCudaAlchLambdas();
     }
 #endif // BONDED_CUDA
 #endif // NAMD_CUDA
     return;
   }
 //fepe
 
   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
     nonbondedScaling = atof(value);
     ComputeNonbondedUtil::select();
     return;
   }
 
   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
     commOnly = atobool(value);
     ComputeNonbondedUtil::select();
     return;
   }
 
   // REST2 - We don't have to make any changes to ComputeNonbondedUtil
   // other than recalculating the LJTable.  Skip doing the other stuff.
   if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) {
     if (!soluteScalingOn) {
       NAMD_die("Cannot set solute scaling factor when soluteScaling is off\n");
     }
     soluteScalingFactor = atof(value);
     if (soluteScalingFactor < 0.0) {
       NAMD_die("Solute scaling factor should be non-negative\n");
     }
     soluteScalingFactorCharge = soluteScalingFactor;
     soluteScalingFactorVdw = soluteScalingFactor;
     // update LJTable for CPU
     ComputeNonbondedUtil::select();
 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
     // update LJTable for GPU, needs CPU update first
     ComputeCUDAMgr::getComputeCUDAMgr()->update();
 #endif
     return;
   }
   if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) {
     soluteScalingFactorVdw = atof(value);
     if (soluteScalingFactorVdw < 0.0) {
       NAMD_die("Solute scaling factor for van der Waals "
           "should be non-negative\n");
     }
     // update LJTable for CPU
     ComputeNonbondedUtil::select();
 #if defined(NAMD_CUDA) || defined(NAMD_HIP)
     // update LJTable for GPU, needs CPU update first
     ComputeCUDAMgr::getComputeCUDAMgr()->update();
 #endif
     return;
   }
   if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) {
     soluteScalingFactorCharge = atof(value);
     if (soluteScalingFactorCharge < 0.0) {
       NAMD_die("Solute scaling factor for electrostatics "
           "should be non-negative\n");
     }
     return;
   }
 
   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
   sprintf(error,"Setting parameter %s from script failed!\n",param);
   NAMD_die(error);
 
 }

◆ send_SimParameters()

void SimParameters::send_SimParameters ( MOStream * msg )

Definition at line 8183 of file SimParameters.C.

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

 {
   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
   if ( msg == NULL )
   {
     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
   }*/
 
   msg->put(sizeof(SimParameters),(char*)this);
   if ( FFTWWisdomString ) {
     int fftwlen = strlen(FFTWWisdomString) + 1;
     msg->put(fftwlen);
     msg->put(fftwlen,FFTWWisdomString);
   }
   if ( tclBCScript ) {
     int tcllen = strlen(tclBCScript) + 1;
     msg->put(tcllen);
     msg->put(tcllen,tclBCScript);
   }
 
 #ifdef MEM_OPT_VERSION
   int filelen = strlen(binAtomFile)+1;
   msg->put(filelen);
   msg->put(filelen, binAtomFile);
 
   filelen = strlen(binCoorFile)+1;
   msg->put(filelen);
   msg->put(filelen, binCoorFile);
 
   if(binVelFile) {
     filelen = strlen(binVelFile)+1;
     msg->put(filelen);
     msg->put(filelen, binVelFile);
   }
 
   if(binRefFile) {
     filelen = strlen(binRefFile)+1;
     msg->put(filelen);
     msg->put(filelen, binRefFile);
   }
 #endif
 
   mgridforcelist.pack_data(msg);
   
   msg->end();
 }

◆ setupIDWS()

int SimParameters::setupIDWS ( )

Definition at line 8310 of file SimParameters.C.

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

                              {
   if (alchLambdaIDWS < 0.) return 0;
   if (alchLambdaIDWS > 1.) {
     NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
   }
  /* 
   * The internal parameter alchIDWSFreq determines the number of steps of MD
   * before each switch of the value of alchLambda2. At most this occurs every
   * time the energy is evaluated and thus the default is the greater of
   * fullElectFrequency and nonbondedFrequency. However, this choice fails to
   * report alternating values if output is printed less often than every step
   * (which is almost certainly true). Thus the frequency is reset to match
   * alchOutFreq or, if that is zero, outputEnergies. Note that, if 
   * alchOutFreq > 0 but != outputEnergies, then the data going to stdout
   * are likely not useful since the comparison value is difficult to infer.
   */
   if ( alchOutFreq % nonbondedFrequency != 0 ) {
     NAMD_die("For IDWS, alchOutFreq must be a multiple of nonBondedFrequency.\n");
   }
   if ( fullElectFrequency > 0 ) {
     if ( alchOutFreq % fullElectFrequency != 0 ) {
       NAMD_die("For IDWS, alchOutFreq must be a multiple of fullElectFrequency.\n");
     }
   }
   if ( alchOutFreq ) {
     alchIDWSFreq = alchOutFreq;
   } else if ( outputEnergies ) {
     alchIDWSFreq = outputEnergies;
   } else {
     NAMD_die("Either alchOutFreq or outputEnergies should be non-zero.\n");
   }
   if ( alchOutFreq && alchOutFreq != outputEnergies) {
     iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS output"
          << " to stdout may not be useful!\n" << endi;
   }
   return 1;
 }

Member Data Documentation

◆ aaAngleExp

int SimParameters::aaAngleExp

Definition at line 1062 of file SimParameters.h.

◆ accelMDalpha

BigReal SimParameters::accelMDalpha

Definition at line 678 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDDebugOn

Bool SimParameters::accelMDDebugOn

Definition at line 673 of file SimParameters.h.

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

◆ accelMDdihe

Bool SimParameters::accelMDdihe

Definition at line 671 of file SimParameters.h.

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

◆ accelMDdual

Bool SimParameters::accelMDdual

Definition at line 672 of file SimParameters.h.

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

◆ accelMDE

BigReal SimParameters::accelMDE

Definition at line 677 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDFirstStep

BigReal SimParameters::accelMDFirstStep

Definition at line 674 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDG

Bool SimParameters::accelMDG

Definition at line 682 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGcMDPrepSteps

int SimParameters::accelMDGcMDPrepSteps

Definition at line 686 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGcMDSteps

int SimParameters::accelMDGcMDSteps

Definition at line 684 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGEquiPrepSteps

int SimParameters::accelMDGEquiPrepSteps

Definition at line 687 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGEquiSteps

int SimParameters::accelMDGEquiSteps

Definition at line 685 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGiE

int SimParameters::accelMDGiE

Definition at line 683 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGresetVaftercmd

Bool SimParameters::accelMDGresetVaftercmd

Definition at line 693 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGRestart

Bool SimParameters::accelMDGRestart

Definition at line 691 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGRestartFile

char SimParameters::accelMDGRestartFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 692 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGSigma0D

BigReal SimParameters::accelMDGSigma0D

Definition at line 690 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGSigma0P

BigReal SimParameters::accelMDGSigma0P

Definition at line 689 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDGStatWindow

int SimParameters::accelMDGStatWindow

Definition at line 688 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDLastStep

BigReal SimParameters::accelMDLastStep

Definition at line 675 of file SimParameters.h.

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

◆ accelMDOn

Bool SimParameters::accelMDOn

Definition at line 670 of file SimParameters.h.

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

◆ accelMDOutFreq

int SimParameters::accelMDOutFreq

Definition at line 676 of file SimParameters.h.

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

◆ accelMDTalpha

BigReal SimParameters::accelMDTalpha

Definition at line 680 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ accelMDTE

BigReal SimParameters::accelMDTE

Definition at line 679 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

◆ adaptTempAutoDt

BigReal SimParameters::adaptTempAutoDt

Definition at line 704 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempBins

int SimParameters::adaptTempBins

Definition at line 705 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempCgamma

BigReal SimParameters::adaptTempCgamma

Definition at line 707 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempDebug

Bool SimParameters::adaptTempDebug

Definition at line 697 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

◆ adaptTempDt

BigReal SimParameters::adaptTempDt

Definition at line 706 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempFirstStep

int SimParameters::adaptTempFirstStep

Definition at line 698 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

◆ adaptTempFreq

int SimParameters::adaptTempFreq

Definition at line 701 of file SimParameters.h.

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

◆ adaptTempInFile

char SimParameters::adaptTempInFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 710 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempLangevin

Bool SimParameters::adaptTempLangevin

Definition at line 708 of file SimParameters.h.

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

◆ adaptTempLastStep

int SimParameters::adaptTempLastStep

Definition at line 699 of file SimParameters.h.

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

◆ adaptTempOn

Bool SimParameters::adaptTempOn

Definition at line 696 of file SimParameters.h.

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

◆ adaptTempOutFreq

int SimParameters::adaptTempOutFreq

Definition at line 700 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

◆ adaptTempRandom

Bool SimParameters::adaptTempRandom

Definition at line 713 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

◆ adaptTempRescale

Bool SimParameters::adaptTempRescale

Definition at line 709 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

◆ adaptTempRestartFile

char SimParameters::adaptTempRestartFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 711 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempRestartFreq

int SimParameters::adaptTempRestartFreq

Definition at line 712 of file SimParameters.h.

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

◆ adaptTempTmax

BigReal SimParameters::adaptTempTmax

Definition at line 703 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ adaptTempTmin

BigReal SimParameters::adaptTempTmin

Definition at line 702 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

◆ alchBondDecouple

Bool SimParameters::alchBondDecouple

Definition at line 475 of file SimParameters.h.

◆ alchBondLambdaEnd

BigReal SimParameters::alchBondLambdaEnd

Definition at line 469 of file SimParameters.h.

◆ alchDecouple

Bool SimParameters::alchDecouple

Definition at line 474 of file SimParameters.h.

◆ alchElecLambdaStart

BigReal SimParameters::alchElecLambdaStart

Definition at line 452 of file SimParameters.h.

◆ alchEnsembleAvg

Bool SimParameters::alchEnsembleAvg

Definition at line 447 of file SimParameters.h.

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

◆ alchEquilSteps

int SimParameters::alchEquilSteps

Definition at line 449 of file SimParameters.h.

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

◆ alchFepOn

Bool SimParameters::alchFepOn

Definition at line 429 of file SimParameters.h.

Referenced by CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeOneDevice::finishReduction(), Controller::outputFepEnergy(), Controller::printEnergies(), and Controller::printFepMessage().

◆ alchFepOnAtStartup

Bool SimParameters::alchFepOnAtStartup

Definition at line 426 of file SimParameters.h.

◆ alchIDWSFreq

int SimParameters::alchIDWSFreq

Definition at line 438 of file SimParameters.h.

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

◆ alchLambda

BigReal SimParameters::alchLambda

Definition at line 435 of file SimParameters.h.

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

◆ alchLambda2

BigReal SimParameters::alchLambda2

Definition at line 436 of file SimParameters.h.

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

◆ alchLambdaFreq

int SimParameters::alchLambdaFreq

Definition at line 439 of file SimParameters.h.

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

◆ alchLambdaIDWS

BigReal SimParameters::alchLambdaIDWS

Definition at line 437 of file SimParameters.h.

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

◆ alchMethod

int SimParameters::alchMethod

Definition at line 434 of file SimParameters.h.

◆ alchOn

Bool SimParameters::alchOn

Definition at line 428 of file SimParameters.h.

Referenced by CudaPmeOneDevice::compute(), WorkDistrib::createAtomLists(), CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeOneDevice::finishReduction(), Sequencer::integrate(), Sequencer::integrate_SOA(), NamdState::loadStructure(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), and Controller::printTiMessage().

◆ alchOnAtStartup

Bool SimParameters::alchOnAtStartup

Definition at line 425 of file SimParameters.h.

◆ alchOutFile

char SimParameters::alchOutFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 448 of file SimParameters.h.

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

◆ alchOutFreq

int SimParameters::alchOutFreq

Definition at line 446 of file SimParameters.h.

Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::outputFepEnergy(), and Controller::outputTiEnergy().

◆ alchRepLambdaEnd

BigReal SimParameters::alchRepLambdaEnd

Definition at line 463 of file SimParameters.h.

◆ alchTemp

BigReal SimParameters::alchTemp

Definition at line 445 of file SimParameters.h.

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

◆ alchThermIntOn

Bool SimParameters::alchThermIntOn

Definition at line 432 of file SimParameters.h.

Referenced by CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeOneDevice::finishReduction(), Controller::outputTiEnergy(), Controller::printEnergies(), and Controller::printTiMessage().

◆ alchThermIntOnAtStartup

Bool SimParameters::alchThermIntOnAtStartup

Definition at line 427 of file SimParameters.h.

◆ alchVdwLambdaEnd

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 458 of file SimParameters.h.

◆ alchVdwShiftCoeff

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 450 of file SimParameters.h.

◆ alchWCAOn

Bool SimParameters::alchWCAOn

Definition at line 433 of file SimParameters.h.

◆ alpha_cutoff

BigReal SimParameters::alpha_cutoff

Definition at line 572 of file SimParameters.h.

◆ alpha_max

BigReal SimParameters::alpha_max

Definition at line 573 of file SimParameters.h.

◆ amberOn

Bool SimParameters::amberOn

Definition at line 1083 of file SimParameters.h.

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

◆ auxFilename

char SimParameters::auxFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 244 of file SimParameters.h.

Referenced by CollectionMaster::receiveDataStream().

◆ benchmarkTime

int SimParameters::benchmarkTime

Definition at line 980 of file SimParameters.h.

Referenced by Controller::printTiming().

◆ benchTimestep

Bool SimParameters::benchTimestep

Definition at line 193 of file SimParameters.h.

◆ berendsenPressureCompressibility

BigReal SimParameters::berendsenPressureCompressibility

Definition at line 737 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

◆ berendsenPressureFreq

int SimParameters::berendsenPressureFreq

Definition at line 739 of file SimParameters.h.

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

◆ berendsenPressureOn

Bool SimParameters::berendsenPressureOn

Definition at line 735 of file SimParameters.h.

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

◆ berendsenPressureRelaxationTime

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 738 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

◆ berendsenPressureTarget

BigReal SimParameters::berendsenPressureTarget

Definition at line 736 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

◆ binaryOutput

Bool SimParameters::binaryOutput

Definition at line 262 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

◆ binaryRestart

Bool SimParameters::binaryRestart

Definition at line 260 of file SimParameters.h.

◆ binAtomFile

char* SimParameters::binAtomFile

Definition at line 1122 of file SimParameters.h.

◆ binCoorFile

char* SimParameters::binCoorFile

Definition at line 1123 of file SimParameters.h.

◆ binRefFile

char* SimParameters::binRefFile

Definition at line 1125 of file SimParameters.h.

◆ binVelFile

char* SimParameters::binVelFile

Definition at line 1124 of file SimParameters.h.

◆ bondedCUDA

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 875 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ bondedGPU

int SimParameters::bondedGPU

replacement keyword for bondedCUDA

Definition at line 880 of file SimParameters.h.

◆ cellBasisVector1

zVector SimParameters::cellBasisVector1

Definition at line 151 of file SimParameters.h.

◆ cellBasisVector2

zVector SimParameters::cellBasisVector2

Definition at line 152 of file SimParameters.h.

◆ cellBasisVector3

zVector SimParameters::cellBasisVector3

Definition at line 153 of file SimParameters.h.

◆ cellOrigin

zVector SimParameters::cellOrigin

Definition at line 154 of file SimParameters.h.

◆ COLDOn

Bool SimParameters::COLDOn

Definition at line 637 of file SimParameters.h.

◆ COLDRate

BigReal SimParameters::COLDRate

Definition at line 639 of file SimParameters.h.

◆ COLDTemp

BigReal SimParameters::COLDTemp

Definition at line 640 of file SimParameters.h.

◆ colvarsOn

Bool SimParameters::colvarsOn

Definition at line 610 of file SimParameters.h.

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

◆ commOnly

Bool SimParameters::commOnly

Definition at line 1020 of file SimParameters.h.

Referenced by Sequencer::integrate().

◆ comMove

Bool SimParameters::comMove

Definition at line 215 of file SimParameters.h.

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

◆ computeEnergies

int SimParameters::computeEnergies

Definition at line 964 of file SimParameters.h.

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

◆ computeMapFilename

char SimParameters::computeMapFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 1131 of file SimParameters.h.

◆ consForceFile

char SimParameters::consForceFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 961 of file SimParameters.h.

◆ consForceOn

Bool SimParameters::consForceOn

Definition at line 960 of file SimParameters.h.

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

◆ consForceScaling

BigReal SimParameters::consForceScaling

Definition at line 962 of file SimParameters.h.

Referenced by ComputeConsForce::doForce().

◆ consTorqueAxisFile

char SimParameters::consTorqueAxisFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 381 of file SimParameters.h.

◆ consTorqueFile

char SimParameters::consTorqueFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 379 of file SimParameters.h.

◆ consTorqueGlobVal

BigReal SimParameters::consTorqueGlobVal

Definition at line 383 of file SimParameters.h.

◆ consTorqueOn

Bool SimParameters::consTorqueOn

Definition at line 378 of file SimParameters.h.

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

◆ consTorquePivotFile

char SimParameters::consTorquePivotFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 382 of file SimParameters.h.

◆ consTorqueValFile

char SimParameters::consTorqueValFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 384 of file SimParameters.h.

◆ constraintExp

int SimParameters::constraintExp

Definition at line 297 of file SimParameters.h.

◆ constraintScaling

BigReal SimParameters::constraintScaling

Definition at line 330 of file SimParameters.h.

◆ constraintsOn

Bool SimParameters::constraintsOn

Definition at line 295 of file SimParameters.h.

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

◆ constrXOn

Bool SimParameters::constrXOn

Definition at line 321 of file SimParameters.h.

◆ constrYOn

Bool SimParameters::constrYOn

Definition at line 321 of file SimParameters.h.

◆ constrZOn

Bool SimParameters::constrZOn

Definition at line 321 of file SimParameters.h.

◆ cosAngles

Bool SimParameters::cosAngles

Definition at line 592 of file SimParameters.h.

◆ coulomb_radius_offset

BigReal SimParameters::coulomb_radius_offset

Definition at line 566 of file SimParameters.h.

◆ cudaGlobalProfilingFreq

int SimParameters::cudaGlobalProfilingFreq

Definition at line 1148 of file SimParameters.h.

◆ CUDASOAintegrate

Bool SimParameters::CUDASOAintegrate

Definition at line 133 of file SimParameters.h.

Referenced by colvarproxy_namd::add_energy(), Sequencer::algorithm(), Controller::calcPressure(), colvarproxy_namd::calculate(), Controller::compareChecksums(), Controller::correctMomentum(), ComputeCUDAMgr::createCudaComputeNonbonded(), ComputeGlobal::doWork(), CudaComputeNonbonded::doWork(), CudaComputeNonbonded::finishPatches(), CudaComputeNonbonded::finishReductions(), Controller::getTotalPotentialEnergy(), Controller::integrate(), Controller::langevinPiston1(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), CudaComputeNonbonded::openBoxesOnPe(), CudaComputeNonbonded::patchReady(), Controller::printEnergies(), Sequencer::rattle1_SOA(), Controller::receivePressure(), ComputeGlobal::recvResults(), Sequencer::runComputeObjects_SOA(), ComputeMgr::sendComputeGlobalData(), ComputeMgr::sendComputeGlobalResults(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ CUDASOAintegrateMode

Bool SimParameters::CUDASOAintegrateMode

mode flag set by "CUDASOAintegrate on" in config file this remains set the same, no matter whether our activity is dynamics or minimization

Definition at line 126 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), ComputeGlobal::doWork(), Sequencer::minimize(), WorkDistrib::patchMapInit(), ComputeGlobal::recvResults(), ComputeGlobal::saveTotalForces(), Sequencer::Sequencer(), and Sequencer::~Sequencer().

◆ cutoff

BigReal SimParameters::cutoff

Definition at line 264 of file SimParameters.h.

Referenced by ComputeQM::initialize(), Sequencer::integrate_SOA(), Sequencer::maximumMove(), and ComputeQMMgr::recvPntChrg().

◆ cylindricalBCAxis

char SimParameters::cylindricalBCAxis

Definition at line 931 of file SimParameters.h.

◆ cylindricalBCexp1

int SimParameters::cylindricalBCexp1

Definition at line 936 of file SimParameters.h.

◆ cylindricalBCexp2

int SimParameters::cylindricalBCexp2

Definition at line 937 of file SimParameters.h.

◆ cylindricalBCk1

BigReal SimParameters::cylindricalBCk1

Definition at line 938 of file SimParameters.h.

◆ cylindricalBCk2

BigReal SimParameters::cylindricalBCk2

Definition at line 939 of file SimParameters.h.

◆ cylindricalBCl1

BigReal SimParameters::cylindricalBCl1

Definition at line 934 of file SimParameters.h.

◆ cylindricalBCl2

BigReal SimParameters::cylindricalBCl2

Definition at line 935 of file SimParameters.h.

◆ cylindricalBCOn

Bool SimParameters::cylindricalBCOn

Definition at line 928 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ cylindricalBCr1

BigReal SimParameters::cylindricalBCr1

Definition at line 932 of file SimParameters.h.

◆ cylindricalBCr2

BigReal SimParameters::cylindricalBCr2

Definition at line 933 of file SimParameters.h.

◆ cylindricalCenter

zVector SimParameters::cylindricalCenter

Definition at line 930 of file SimParameters.h.

◆ daCutoffDist

BigReal SimParameters::daCutoffDist

Definition at line 1069 of file SimParameters.h.

◆ daOffDist

BigReal SimParameters::daOffDist

Definition at line 1069 of file SimParameters.h.

◆ daOnDist

BigReal SimParameters::daOnDist

Definition at line 1069 of file SimParameters.h.

◆ dcdFilename

char SimParameters::dcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 245 of file SimParameters.h.

◆ dcdFrequency

int SimParameters::dcdFrequency

Definition at line 234 of file SimParameters.h.

Referenced by Sequencer::integrate_SOA().

◆ dcdSelectionOn

int SimParameters::dcdSelectionOn

Definition at line 243 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ dcdUnitCell

int SimParameters::dcdUnitCell

Definition at line 236 of file SimParameters.h.

◆ dhaCutoffAngle

BigReal SimParameters::dhaCutoffAngle

Definition at line 1065 of file SimParameters.h.

◆ dhaOffAngle

BigReal SimParameters::dhaOffAngle

Definition at line 1065 of file SimParameters.h.

◆ dhaOnAngle

BigReal SimParameters::dhaOnAngle

Definition at line 1065 of file SimParameters.h.

◆ dielectric

BigReal SimParameters::dielectric

Definition at line 222 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ dihedralOn

Bool SimParameters::dihedralOn

Definition at line 636 of file SimParameters.h.

◆ disableTopology

Bool SimParameters::disableTopology

Definition at line 190 of file SimParameters.h.

◆ distAttExp

int SimParameters::distAttExp

Definition at line 1062 of file SimParameters.h.

◆ distRepExp

int SimParameters::distRepExp

Definition at line 1062 of file SimParameters.h.

◆ drudeBondConst

BigReal SimParameters::drudeBondConst

Definition at line 584 of file SimParameters.h.

◆ drudeBondLen

BigReal SimParameters::drudeBondLen

Definition at line 582 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

◆ drudeDamping

BigReal SimParameters::drudeDamping

Definition at line 580 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ drudeHardWallOn

Bool SimParameters::drudeHardWallOn

Definition at line 578 of file SimParameters.h.

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

◆ drudeNbtholeCut

BigReal SimParameters::drudeNbtholeCut

Definition at line 585 of file SimParameters.h.

◆ drudeOn

Bool SimParameters::drudeOn

Definition at line 577 of file SimParameters.h.

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

◆ drudeTemp

BigReal SimParameters::drudeTemp

Definition at line 579 of file SimParameters.h.

Referenced by Sequencer::langevinVelocitiesBBK2().

◆ dt

BigReal SimParameters::dt

Definition at line 147 of file SimParameters.h.

Referenced by Controller::berendsenPressure(), colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::multigratorPressure(), Controller::multigratorTemperature(), Controller::printEnergies(), Controller::printTiming(), ComputeQMMgr::recvPartQM(), and colvarproxy_namd::setup().

◆ eField

zVector SimParameters::eField

Definition at line 943 of file SimParameters.h.

◆ eFieldFreq

BigReal SimParameters::eFieldFreq

Definition at line 944 of file SimParameters.h.

◆ eFieldNormalized

Bool SimParameters::eFieldNormalized

Definition at line 942 of file SimParameters.h.

◆ eFieldOn

Bool SimParameters::eFieldOn

Definition at line 941 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ eFieldPhase

BigReal SimParameters::eFieldPhase

Definition at line 945 of file SimParameters.h.

◆ emptyPatchLoad

int SimParameters::emptyPatchLoad

Definition at line 1038 of file SimParameters.h.

◆ exclude

ExclusionSettings SimParameters::exclude

Definition at line 223 of file SimParameters.h.

Referenced by buildExclusions().

◆ excludeFromPressure

Bool SimParameters::excludeFromPressure

Definition at line 724 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ extCoordFilename

char SimParameters::extCoordFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 501 of file SimParameters.h.

◆ extForceFilename

char SimParameters::extForceFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 502 of file SimParameters.h.

◆ extForcesCommand

char SimParameters::extForcesCommand[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 500 of file SimParameters.h.

◆ extForcesOn

Bool SimParameters::extForcesOn

Definition at line 499 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ extraBondsCosAngles

Bool SimParameters::extraBondsCosAngles

Definition at line 957 of file SimParameters.h.

◆ extraBondsCosAnglesSetByUser

Bool SimParameters::extraBondsCosAnglesSetByUser

Definition at line 958 of file SimParameters.h.

◆ extraBondsOn

Bool SimParameters::extraBondsOn

Definition at line 956 of file SimParameters.h.

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

◆ FFTWEstimate

Bool SimParameters::FFTWEstimate

Definition at line 897 of file SimParameters.h.

◆ FFTWPatient

Bool SimParameters::FFTWPatient

Definition at line 898 of file SimParameters.h.

◆ FFTWUseWisdom

Bool SimParameters::FFTWUseWisdom

Definition at line 899 of file SimParameters.h.

◆ FFTWWisdomFile

char SimParameters::FFTWWisdomFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 900 of file SimParameters.h.

◆ FFTWWisdomString

char* SimParameters::FFTWWisdomString

Definition at line 901 of file SimParameters.h.

◆ firstLdbStep

int SimParameters::firstLdbStep

Definition at line 167 of file SimParameters.h.

Referenced by Controller::printEnergies().

◆ firstTimestep

◆ fixCellDims

Bool SimParameters::fixCellDims

Definition at line 730 of file SimParameters.h.

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

◆ fixCellDimX

Bool SimParameters::fixCellDimX

Definition at line 731 of file SimParameters.h.

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

◆ fixCellDimY

Bool SimParameters::fixCellDimY

Definition at line 732 of file SimParameters.h.

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

◆ fixCellDimZ

Bool SimParameters::fixCellDimZ

Definition at line 733 of file SimParameters.h.

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

◆ fixedAtomsForceOutput

Bool SimParameters::fixedAtomsForceOutput

Definition at line 614 of file SimParameters.h.

Referenced by CollectionMgr::submitForces().

◆ fixedAtomsForces

Bool SimParameters::fixedAtomsForces

Definition at line 613 of file SimParameters.h.

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

◆ fixedAtomsOn

◆ FMAFFTBlock

int SimParameters::FMAFFTBlock

Definition at line 786 of file SimParameters.h.

◆ FMAFFTOn

Bool SimParameters::FMAFFTOn

Definition at line 785 of file SimParameters.h.

◆ FMALevels

int SimParameters::FMALevels

Definition at line 783 of file SimParameters.h.

◆ FMAMp

int SimParameters::FMAMp

Definition at line 784 of file SimParameters.h.

◆ FMAOn

Bool SimParameters::FMAOn

Definition at line 782 of file SimParameters.h.

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

◆ fmaTheta

BigReal SimParameters::fmaTheta

Definition at line 163 of file SimParameters.h.

◆ FMMLevels

int SimParameters::FMMLevels

Definition at line 830 of file SimParameters.h.

◆ FMMOn

Bool SimParameters::FMMOn

Definition at line 829 of file SimParameters.h.

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

◆ FMMPadding

BigReal SimParameters::FMMPadding

Definition at line 831 of file SimParameters.h.

◆ forceDcdFilename

char SimParameters::forceDcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 247 of file SimParameters.h.

◆ forceDcdFrequency

int SimParameters::forceDcdFrequency

Definition at line 239 of file SimParameters.h.

Referenced by Sequencer::integrate_SOA().

◆ freeEnergyOn

Bool SimParameters::freeEnergyOn

Definition at line 608 of file SimParameters.h.

◆ fsMax

BigReal SimParameters::fsMax

Definition at line 563 of file SimParameters.h.

◆ fullDirectOn

Bool SimParameters::fullDirectOn

Definition at line 788 of file SimParameters.h.

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

◆ fullDispersionFrequency

int SimParameters::fullDispersionFrequency

Definition at line 161 of file SimParameters.h.

◆ fullElectFrequency

int SimParameters::fullElectFrequency

Definition at line 159 of file SimParameters.h.

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

◆ gbis_beta

BigReal SimParameters::gbis_beta

Definition at line 570 of file SimParameters.h.

◆ gbis_delta

BigReal SimParameters::gbis_delta

Definition at line 569 of file SimParameters.h.

◆ gbis_gamma

BigReal SimParameters::gbis_gamma

Definition at line 571 of file SimParameters.h.

◆ GBISOn

Bool SimParameters::GBISOn

Definition at line 562 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), ComputeCUDAMgr::createCudaComputeNonbonded(), CudaComputeNonbonded::finishReductions(), Sequencer::integrate(), and Sequencer::minimize().

◆ GBISserOn

Bool SimParameters::GBISserOn

Definition at line 564 of file SimParameters.h.

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

◆ genCompressedPsf

Bool SimParameters::genCompressedPsf

Definition at line 1106 of file SimParameters.h.

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

◆ globalForcesOn

Bool SimParameters::globalForcesOn

Definition at line 593 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ globalMasterFrequency

int SimParameters::globalMasterFrequency

How frequently (time steps) global master (i.e., colvars, tclForces, etc. is called. Default value 1.

Definition at line 595 of file SimParameters.h.

Referenced by ComputeGlobal::doWork(), GlobalMasterServer::GlobalMasterServer(), and ComputeGlobal::recvResults().

◆ globalMasterScaleByFrequency

Bool SimParameters::globalMasterScaleByFrequency

Scale globalMaster forces by a factor of frequency? Default value off.

Definition at line 597 of file SimParameters.h.

Referenced by ComputeGlobal::recvResults().

◆ globalMasterStaleForces

Bool SimParameters::globalMasterStaleForces

Do MTS by the stale forces method instead of scaling by frequency. Default off.

Definition at line 599 of file SimParameters.h.

◆ globalOn

Bool SimParameters::globalOn

Definition at line 635 of file SimParameters.h.

◆ goCoordinates

char SimParameters::goCoordinates[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 341 of file SimParameters.h.

◆ goForcesOn

Bool SimParameters::goForcesOn

Definition at line 339 of file SimParameters.h.

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

◆ goGroPair

Bool SimParameters::goGroPair

Definition at line 338 of file SimParameters.h.

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

◆ goMethod

GoChoices SimParameters::goMethod

Definition at line 343 of file SimParameters.h.

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

◆ goParameters

char SimParameters::goParameters[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 340 of file SimParameters.h.

◆ GPUresidentMode

Bool SimParameters::GPUresidentMode

"GPUresident on" will be replacing "CUDASOAintegrate on"

Definition at line 130 of file SimParameters.h.

◆ gridforcechecksize

Bool SimParameters::gridforcechecksize

Definition at line 308 of file SimParameters.h.

◆ gridforceContA1

Bool SimParameters::gridforceContA1

Definition at line 303 of file SimParameters.h.

◆ gridforceContA2

Bool SimParameters::gridforceContA2

Definition at line 304 of file SimParameters.h.

◆ gridforceContA3

Bool SimParameters::gridforceContA3

Definition at line 305 of file SimParameters.h.

◆ gridforceLite

Bool SimParameters::gridforceLite

Definition at line 307 of file SimParameters.h.

◆ gridforceOn

Bool SimParameters::gridforceOn

Definition at line 300 of file SimParameters.h.

◆ gridforceScale

zVector SimParameters::gridforceScale

Definition at line 302 of file SimParameters.h.

◆ gridforceVOffset

zVector SimParameters::gridforceVOffset

Definition at line 306 of file SimParameters.h.

◆ gridforceVolts

Bool SimParameters::gridforceVolts

Definition at line 301 of file SimParameters.h.

◆ gromacsOn

Bool SimParameters::gromacsOn

Definition at line 1089 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ groupRestraints

GroupRestraintList SimParameters::groupRestraints

Definition at line 315 of file SimParameters.h.

◆ groupRestraintsOn

Bool SimParameters::groupRestraintsOn

Definition at line 314 of file SimParameters.h.

◆ haAngleExp

int SimParameters::haAngleExp

Definition at line 1062 of file SimParameters.h.

◆ hgroupCutoff

BigReal SimParameters::hgroupCutoff

Definition at line 1004 of file SimParameters.h.

◆ hybridGroupSize

int SimParameters::hybridGroupSize

Definition at line 171 of file SimParameters.h.

◆ HydrogenBonds

Bool SimParameters::HydrogenBonds

Definition at line 1052 of file SimParameters.h.

◆ ignoreMass

Bool SimParameters::ignoreMass

Definition at line 1001 of file SimParameters.h.

◆ IMDfreq

int SimParameters::IMDfreq

Definition at line 1074 of file SimParameters.h.

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

◆ IMDignore

int SimParameters::IMDignore

Definition at line 1077 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

◆ IMDignoreForces

int SimParameters::IMDignoreForces

Definition at line 1079 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

◆ IMDon

int SimParameters::IMDon

Definition at line 1072 of file SimParameters.h.

Referenced by Controller::printEnergies().

◆ IMDport

int SimParameters::IMDport

Definition at line 1073 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

◆ IMDwait

int SimParameters::IMDwait

Definition at line 1075 of file SimParameters.h.

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

◆ initialTemp

BigReal SimParameters::initialTemp

Definition at line 213 of file SimParameters.h.

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

◆ ion_concentration

BigReal SimParameters::ion_concentration

Definition at line 568 of file SimParameters.h.

◆ kappa

BigReal SimParameters::kappa

Definition at line 567 of file SimParameters.h.

◆ langevin_useBAOAB

Bool SimParameters::langevin_useBAOAB

Definition at line 625 of file SimParameters.h.

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

◆ langevinDamping

BigReal SimParameters::langevinDamping

Definition at line 619 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ langevinGammasDiffer

Bool SimParameters::langevinGammasDiffer

Flag set internally - when all gammas are identical we can avoid extra call to satisfy rigid bond constraints.

Definition at line 621 of file SimParameters.h.

Referenced by Sequencer::langevinVelocitiesBBK2_SOA().

◆ langevinHydrogen

Bool SimParameters::langevinHydrogen

Definition at line 620 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ langevinOn

Bool SimParameters::langevinOn

Definition at line 617 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2(), Sequencer::langevinVelocitiesBBK2_SOA(), NamdState::loadStructure(), Controller::receivePressure(), and colvarproxy_namd::update_target_temperature().

◆ langevinOnAtStartup

Bool SimParameters::langevinOnAtStartup

Definition at line 616 of file SimParameters.h.

◆ langevinPistonBarrier

Bool SimParameters::langevinPistonBarrier

Definition at line 742 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

◆ langevinPistonDecay

BigReal SimParameters::langevinPistonDecay

Definition at line 745 of file SimParameters.h.

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

◆ langevinPistonOn

Bool SimParameters::langevinPistonOn

Definition at line 741 of file SimParameters.h.

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

◆ langevinPistonPeriod

BigReal SimParameters::langevinPistonPeriod

Definition at line 744 of file SimParameters.h.

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

◆ langevinPistonTarget

BigReal SimParameters::langevinPistonTarget

Definition at line 743 of file SimParameters.h.

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

◆ langevinPistonTemp

BigReal SimParameters::langevinPistonTemp

Definition at line 746 of file SimParameters.h.

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

◆ langevinTemp

BigReal SimParameters::langevinTemp

Definition at line 618 of file SimParameters.h.

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

◆ lastLdbStep

int SimParameters::lastLdbStep

Definition at line 169 of file SimParameters.h.

◆ lattice

Lattice SimParameters::lattice

Definition at line 155 of file SimParameters.h.

Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), GlobalMasterServer::GlobalMasterServer(), Patch::Patch(), WorkDistrib::patchMapInit(), PatchMgr::setLattice(), and Node::startup().

◆ LCPOOn

Bool SimParameters::LCPOOn

Definition at line 574 of file SimParameters.h.

Referenced by Sequencer::integrate(), WorkDistrib::mapComputes(), Sequencer::minimize(), and WorkDistrib::patchMapInit().

◆ ldBalancer

int SimParameters::ldBalancer

Definition at line 164 of file SimParameters.h.

◆ ldbBackgroundScaling

BigReal SimParameters::ldbBackgroundScaling

Definition at line 172 of file SimParameters.h.

◆ ldbHomeBackgroundScaling

BigReal SimParameters::ldbHomeBackgroundScaling

Definition at line 174 of file SimParameters.h.

◆ ldbPeriod

int SimParameters::ldbPeriod

Definition at line 166 of file SimParameters.h.

◆ ldbPMEBackgroundScaling

BigReal SimParameters::ldbPMEBackgroundScaling

Definition at line 173 of file SimParameters.h.

◆ ldbRelativeGrainsize

BigReal SimParameters::ldbRelativeGrainsize

Definition at line 175 of file SimParameters.h.

◆ ldbStrategy

int SimParameters::ldbStrategy

Definition at line 165 of file SimParameters.h.

◆ ldbUnloadOne

Bool SimParameters::ldbUnloadOne

Definition at line 207 of file SimParameters.h.

◆ ldbUnloadOutputPEs

Bool SimParameters::ldbUnloadOutputPEs

Definition at line 208 of file SimParameters.h.

◆ ldbUnloadPME

Bool SimParameters::ldbUnloadPME

Definition at line 205 of file SimParameters.h.

◆ ldbUnloadZero

Bool SimParameters::ldbUnloadZero

Definition at line 206 of file SimParameters.h.

◆ lesFactor

int SimParameters::lesFactor

Definition at line 481 of file SimParameters.h.

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

◆ lesOn

Bool SimParameters::lesOn

Definition at line 480 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().

◆ lesReduceMass

Bool SimParameters::lesReduceMass

Definition at line 483 of file SimParameters.h.

◆ lesReduceTemp

Bool SimParameters::lesReduceTemp

Definition at line 482 of file SimParameters.h.

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

◆ limitDist

BigReal SimParameters::limitDist

Definition at line 271 of file SimParameters.h.

◆ lincsOn

int SimParameters::lincsOn

Definition at line 111 of file SimParameters.h.

◆ LJcorrection

Bool SimParameters::LJcorrection

Definition at line 145 of file SimParameters.h.

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

◆ LJcorrectionAlt

Bool SimParameters::LJcorrectionAlt

Definition at line 146 of file SimParameters.h.

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

◆ LJPMEEwaldCoefficient

BigReal SimParameters::LJPMEEwaldCoefficient

Definition at line 836 of file SimParameters.h.

◆ LJPMEGridSizeX

int SimParameters::LJPMEGridSizeX

Definition at line 838 of file SimParameters.h.

◆ LJPMEGridSizeY

int SimParameters::LJPMEGridSizeY

Definition at line 839 of file SimParameters.h.

◆ LJPMEGridSizeZ

int SimParameters::LJPMEGridSizeZ

Definition at line 840 of file SimParameters.h.

◆ LJPMEGridSpacing

BigReal SimParameters::LJPMEGridSpacing

Definition at line 841 of file SimParameters.h.

◆ LJPMEInterpOrder

int SimParameters::LJPMEInterpOrder

Definition at line 837 of file SimParameters.h.

◆ LJPMEOn

Bool SimParameters::LJPMEOn

Definition at line 834 of file SimParameters.h.

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

◆ LJPMETolerance

BigReal SimParameters::LJPMETolerance

Definition at line 835 of file SimParameters.h.

◆ loadComputeMap

Bool SimParameters::loadComputeMap

Definition at line 1133 of file SimParameters.h.

◆ lonepairs

Bool SimParameters::lonepairs

Definition at line 142 of file SimParameters.h.

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

◆ longSplitting

int SimParameters::longSplitting

Definition at line 998 of file SimParameters.h.

◆ loweAndersenCutoff

BigReal SimParameters::loweAndersenCutoff

Definition at line 632 of file SimParameters.h.

◆ loweAndersenOn

Bool SimParameters::loweAndersenOn

Definition at line 629 of file SimParameters.h.

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

◆ loweAndersenRate

BigReal SimParameters::loweAndersenRate

Definition at line 631 of file SimParameters.h.

◆ loweAndersenTemp

BigReal SimParameters::loweAndersenTemp

Definition at line 630 of file SimParameters.h.

Referenced by colvarproxy_namd::update_target_temperature().

◆ mallocTest

Bool SimParameters::mallocTest

Definition at line 1110 of file SimParameters.h.

Referenced by Node::startup().

◆ margin

BigReal SimParameters::margin

Definition at line 265 of file SimParameters.h.

◆ martiniDielAllow

Bool SimParameters::martiniDielAllow

Definition at line 281 of file SimParameters.h.

◆ martiniSwitching

Bool SimParameters::martiniSwitching

Definition at line 279 of file SimParameters.h.

◆ maxExclusionFlags

int SimParameters::maxExclusionFlags

Definition at line 1040 of file SimParameters.h.

◆ maximumMove

BigReal SimParameters::maximumMove

Definition at line 913 of file SimParameters.h.

Referenced by Sequencer::maximumMove().

◆ maxPairPart

int SimParameters::maxPairPart

Definition at line 1026 of file SimParameters.h.

◆ maxPatches

int SimParameters::maxPatches

Definition at line 204 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ maxSelfPart

int SimParameters::maxSelfPart

Definition at line 1024 of file SimParameters.h.

◆ mergeCrossterms

Bool SimParameters::mergeCrossterms

Definition at line 990 of file SimParameters.h.

Referenced by Controller::printEnergies().

◆ mgridforcelist

MGridforceParamsList SimParameters::mgridforcelist

Definition at line 311 of file SimParameters.h.

Referenced by colvarproxy_namd::check_volmap_by_name(), colvarproxy_namd::get_volmap_id_from_name(), colvarproxy_namd::init_volmap_by_name(), Node::reloadGridforceGrid(), and Node::updateGridScale().

◆ mgridforceOn

Bool SimParameters::mgridforceOn

Definition at line 310 of file SimParameters.h.

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

◆ mic_deviceThreshold

int SimParameters::mic_deviceThreshold

Definition at line 1141 of file SimParameters.h.

◆ mic_hostSplit

int SimParameters::mic_hostSplit

Definition at line 1136 of file SimParameters.h.

◆ mic_numParts_pair_p1

int SimParameters::mic_numParts_pair_p1

Definition at line 1138 of file SimParameters.h.

◆ mic_numParts_pair_p2

int SimParameters::mic_numParts_pair_p2

Definition at line 1139 of file SimParameters.h.

◆ mic_numParts_self_p1

int SimParameters::mic_numParts_self_p1

Definition at line 1137 of file SimParameters.h.

◆ mic_singleKernel

int SimParameters::mic_singleKernel

Definition at line 1142 of file SimParameters.h.

◆ mic_unloadMICPEs

int SimParameters::mic_unloadMICPEs

Definition at line 1140 of file SimParameters.h.

◆ minAtomsPerPatch

int SimParameters::minAtomsPerPatch

Definition at line 1036 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ minBabyStep

BigReal SimParameters::minBabyStep

Definition at line 910 of file SimParameters.h.

◆ minimizeCGOn

Bool SimParameters::minimizeCGOn

Definition at line 907 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ minimizeOn

Bool SimParameters::minimizeOn

Definition at line 912 of file SimParameters.h.

Referenced by Sequencer::minimizationQuenchVelocity().

◆ minLineGoal

BigReal SimParameters::minLineGoal

Definition at line 911 of file SimParameters.h.

Referenced by Controller::minimize().

◆ minTinyStep

BigReal SimParameters::minTinyStep

Definition at line 909 of file SimParameters.h.

◆ minVerbose

Bool SimParameters::minVerbose

Definition at line 908 of file SimParameters.h.

Referenced by Controller::minimize().

◆ miscForcesOn

Bool SimParameters::miscForcesOn

Definition at line 609 of file SimParameters.h.

◆ mollyIter

int SimParameters::mollyIter

Definition at line 1008 of file SimParameters.h.

◆ mollyOn

int SimParameters::mollyOn

Definition at line 1006 of file SimParameters.h.

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

◆ mollyTol

BigReal SimParameters::mollyTol

Definition at line 1007 of file SimParameters.h.

◆ monteCarloAcceptanceRate

BigReal SimParameters::monteCarloAcceptanceRate

Definition at line 752 of file SimParameters.h.

Referenced by Controller::monteCarloPressure_accept().

◆ monteCarloAdjustmentFreq

int SimParameters::monteCarloAdjustmentFreq

Definition at line 754 of file SimParameters.h.

Referenced by Controller::monteCarloPressure_accept().

◆ monteCarloMaxVolume

zVector SimParameters::monteCarloMaxVolume

Definition at line 753 of file SimParameters.h.

Referenced by Controller::Controller().

◆ monteCarloPressureFreq

int SimParameters::monteCarloPressureFreq

Definition at line 755 of file SimParameters.h.

Referenced by Controller::monteCarloPressure_accept(), and Controller::monteCarloPressure_prepare().

◆ monteCarloPressureOn

Bool SimParameters::monteCarloPressureOn

Definition at line 749 of file SimParameters.h.

Referenced by Controller::Controller(), NamdState::loadStructure(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().

◆ monteCarloPressureOnAtStartup

Bool SimParameters::monteCarloPressureOnAtStartup

Definition at line 748 of file SimParameters.h.

◆ monteCarloPressureTarget

BigReal SimParameters::monteCarloPressureTarget

Definition at line 750 of file SimParameters.h.

Referenced by Controller::monteCarloPressure_accept().

◆ monteCarloTemp

BigReal SimParameters::monteCarloTemp

Definition at line 751 of file SimParameters.h.

Referenced by Controller::monteCarloPressure_accept().

◆ movDragFile

char SimParameters::movDragFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 361 of file SimParameters.h.

◆ movDragGlobVel

BigReal SimParameters::movDragGlobVel

Definition at line 363 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

◆ movDragOn

Bool SimParameters::movDragOn

Definition at line 360 of file SimParameters.h.

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

◆ movDragVelFile

char SimParameters::movDragVelFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 364 of file SimParameters.h.

◆ movingAverageWindowSize

int SimParameters::movingAverageWindowSize

Definition at line 136 of file SimParameters.h.

Referenced by Controller::resetMovingAverage().

◆ movingConstraintsOn

Bool SimParameters::movingConstraintsOn

Definition at line 347 of file SimParameters.h.

◆ movingConsVel

zVector SimParameters::movingConsVel

Definition at line 349 of file SimParameters.h.

◆ mshakeOn

int SimParameters::mshakeOn

Definition at line 110 of file SimParameters.h.

◆ MSMApprox

int SimParameters::MSMApprox

Definition at line 798 of file SimParameters.h.

◆ MSMBlockSizeX

int SimParameters::MSMBlockSizeX

Definition at line 808 of file SimParameters.h.

◆ MSMBlockSizeY

int SimParameters::MSMBlockSizeY

Definition at line 809 of file SimParameters.h.

◆ MSMBlockSizeZ

int SimParameters::MSMBlockSizeZ

Definition at line 810 of file SimParameters.h.

◆ MSMGridSpacing

BigReal SimParameters::MSMGridSpacing

Definition at line 812 of file SimParameters.h.

◆ MSMLevels

int SimParameters::MSMLevels

Definition at line 804 of file SimParameters.h.

◆ MSMOn

Bool SimParameters::MSMOn

Definition at line 791 of file SimParameters.h.

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

◆ MSMPadding

BigReal SimParameters::MSMPadding

Definition at line 814 of file SimParameters.h.

◆ MSMQuality

int SimParameters::MSMQuality

Definition at line 794 of file SimParameters.h.

◆ MsmSerialOn

Bool SimParameters::MsmSerialOn

Definition at line 827 of file SimParameters.h.

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

◆ MSMSplit

int SimParameters::MSMSplit

Definition at line 801 of file SimParameters.h.

◆ MSMxmax

BigReal SimParameters::MSMxmax

Definition at line 821 of file SimParameters.h.

◆ MSMxmin

BigReal SimParameters::MSMxmin

Definition at line 820 of file SimParameters.h.

◆ MSMymax

BigReal SimParameters::MSMymax

Definition at line 823 of file SimParameters.h.

◆ MSMymin

BigReal SimParameters::MSMymin

Definition at line 822 of file SimParameters.h.

◆ MSMzmax

BigReal SimParameters::MSMzmax

Definition at line 825 of file SimParameters.h.

◆ MSMzmin

BigReal SimParameters::MSMzmin

Definition at line 824 of file SimParameters.h.

◆ MTSAlgorithm

MTSChoices SimParameters::MTSAlgorithm

Definition at line 995 of file SimParameters.h.

Referenced by Sequencer::integrate().

◆ multigratorNoseHooverChainLength

int SimParameters::multigratorNoseHooverChainLength

Definition at line 764 of file SimParameters.h.

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

◆ multigratorOn

Bool SimParameters::multigratorOn

Definition at line 757 of file SimParameters.h.

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

◆ multigratorPressureFreq

int SimParameters::multigratorPressureFreq

Definition at line 760 of file SimParameters.h.

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

◆ multigratorPressureRelaxationTime

BigReal SimParameters::multigratorPressureRelaxationTime

Definition at line 759 of file SimParameters.h.

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

◆ multigratorPressureTarget

BigReal SimParameters::multigratorPressureTarget

Definition at line 758 of file SimParameters.h.

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

◆ multigratorTemperatureFreq

int SimParameters::multigratorTemperatureFreq

Definition at line 763 of file SimParameters.h.

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

◆ multigratorTemperatureRelaxationTime

BigReal SimParameters::multigratorTemperatureRelaxationTime

Definition at line 762 of file SimParameters.h.

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

◆ multigratorTemperatureTarget

BigReal SimParameters::multigratorTemperatureTarget

Definition at line 761 of file SimParameters.h.

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

◆ N

int SimParameters::N

Definition at line 148 of file SimParameters.h.

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

◆ nonbondedFrequency

int SimParameters::nonbondedFrequency

Definition at line 157 of file SimParameters.h.

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

◆ nonbondedScaling

BigReal SimParameters::nonbondedScaling

Definition at line 233 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ noPatchesOnOne

Bool SimParameters::noPatchesOnOne

Definition at line 211 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ noPatchesOnOutputPEs

Bool SimParameters::noPatchesOnOutputPEs

Definition at line 210 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ noPatchesOnZero

Bool SimParameters::noPatchesOnZero

Definition at line 209 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ nsPerDayOn

Bool SimParameters::nsPerDayOn

Definition at line 139 of file SimParameters.h.

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

◆ numAtomsPair

int SimParameters::numAtomsPair

Definition at line 1032 of file SimParameters.h.

◆ numAtomsPair2

int SimParameters::numAtomsPair2

Definition at line 1034 of file SimParameters.h.

◆ numAtomsSelf

int SimParameters::numAtomsSelf

Definition at line 1028 of file SimParameters.h.

◆ numAtomsSelf2

int SimParameters::numAtomsSelf2

Definition at line 1030 of file SimParameters.h.

◆ numinputprocs

int SimParameters::numinputprocs

Definition at line 1121 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ numoutputprocs

int SimParameters::numoutputprocs

Definition at line 1128 of file SimParameters.h.

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

◆ numoutputwrts

int SimParameters::numoutputwrts

Definition at line 1129 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ numTraceSteps

int SimParameters::numTraceSteps

Definition at line 178 of file SimParameters.h.

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

◆ oldParmReader

Bool SimParameters::oldParmReader

Definition at line 1084 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ outputCudaTiming

int SimParameters::outputCudaTiming

Definition at line 984 of file SimParameters.h.

◆ outputEnergies

int SimParameters::outputEnergies

Definition at line 965 of file SimParameters.h.

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

◆ outputEnergiesPrecision

int SimParameters::outputEnergiesPrecision

Definition at line 968 of file SimParameters.h.

Referenced by Controller::printEnergies().

◆ outputFilename

char SimParameters::outputFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 249 of file SimParameters.h.

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

◆ outputMaps

Bool SimParameters::outputMaps

Definition at line 186 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

◆ outputMomenta

int SimParameters::outputMomenta

Definition at line 970 of file SimParameters.h.

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

◆ outputPairlists

int SimParameters::outputPairlists

Definition at line 293 of file SimParameters.h.

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

◆ outputPatchDetails

Bool SimParameters::outputPatchDetails

Definition at line 1042 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

◆ outputPerformance

Bool SimParameters::outputPerformance

Definition at line 976 of file SimParameters.h.

Referenced by Controller::printTiming().

◆ outputPressure

int SimParameters::outputPressure

Definition at line 987 of file SimParameters.h.

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

◆ outputTiming

int SimParameters::outputTiming

Definition at line 973 of file SimParameters.h.

Referenced by Controller::printTiming().

◆ pairInteractionGroup1

int SimParameters::pairInteractionGroup1

Definition at line 588 of file SimParameters.h.

◆ pairInteractionGroup2

int SimParameters::pairInteractionGroup2

Definition at line 589 of file SimParameters.h.

◆ pairInteractionOn

Bool SimParameters::pairInteractionOn

Definition at line 587 of file SimParameters.h.

Referenced by Sequencer::calcKineticEnergy(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), Controller::printEnergies(), Controller::receivePressure(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

◆ pairInteractionSelf

Bool SimParameters::pairInteractionSelf

Definition at line 590 of file SimParameters.h.

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

◆ pairlistDist

BigReal SimParameters::pairlistDist

Definition at line 283 of file SimParameters.h.

◆ pairlistGrow

BigReal SimParameters::pairlistGrow

Definition at line 291 of file SimParameters.h.

◆ pairlistMinProcs

int SimParameters::pairlistMinProcs

Definition at line 285 of file SimParameters.h.

◆ pairlistShrink

BigReal SimParameters::pairlistShrink

Definition at line 290 of file SimParameters.h.

◆ pairlistsPerCycle

int SimParameters::pairlistsPerCycle

Definition at line 289 of file SimParameters.h.

Referenced by Sequencer::Sequencer().

◆ pairlistTrigger

BigReal SimParameters::pairlistTrigger

Definition at line 292 of file SimParameters.h.

◆ paraTypeCharmmOn

Bool SimParameters::paraTypeCharmmOn

Definition at line 334 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ paraTypeXplorOn

Bool SimParameters::paraTypeXplorOn

Definition at line 333 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ patchDimension

BigReal SimParameters::patchDimension

Definition at line 266 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ PMEBarrier

Bool SimParameters::PMEBarrier

Definition at line 858 of file SimParameters.h.

◆ PMEEwaldCoefficient

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 849 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ PMEGridSizeX

int SimParameters::PMEGridSizeX

Definition at line 851 of file SimParameters.h.

◆ PMEGridSizeY

int SimParameters::PMEGridSizeY

Definition at line 852 of file SimParameters.h.

◆ PMEGridSizeZ

int SimParameters::PMEGridSizeZ

Definition at line 853 of file SimParameters.h.

◆ PMEGridSpacing

BigReal SimParameters::PMEGridSpacing

Definition at line 854 of file SimParameters.h.

◆ PMEInterpOrder

int SimParameters::PMEInterpOrder

Definition at line 850 of file SimParameters.h.

◆ PMEMinPoints

int SimParameters::PMEMinPoints

Definition at line 857 of file SimParameters.h.

◆ PMEMinSlices

int SimParameters::PMEMinSlices

Definition at line 856 of file SimParameters.h.

◆ PMEOffload

Bool SimParameters::PMEOffload

Definition at line 866 of file SimParameters.h.

Referenced by PmePencil< CBase_PmeZPencil >::order_init().

◆ PMEOn

Bool SimParameters::PMEOn

Definition at line 847 of file SimParameters.h.

Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), Molecule::prepare_qm(), Controller::printEnergies(), ComputeQMMgr::procQMRes(), ComputeQMMgr::recvPntChrg(), Node::resendMolecule(), and Node::startup().

◆ PMEPencils

int SimParameters::PMEPencils

Definition at line 859 of file SimParameters.h.

◆ PMEPencilsX

int SimParameters::PMEPencilsX

Definition at line 860 of file SimParameters.h.

◆ PMEPencilsXLayout

int SimParameters::PMEPencilsXLayout

Definition at line 864 of file SimParameters.h.

◆ PMEPencilsY

int SimParameters::PMEPencilsY

Definition at line 861 of file SimParameters.h.

◆ PMEPencilsYLayout

int SimParameters::PMEPencilsYLayout

Definition at line 863 of file SimParameters.h.

◆ PMEPencilsZ

int SimParameters::PMEPencilsZ

Definition at line 862 of file SimParameters.h.

◆ PMEProcessors

int SimParameters::PMEProcessors

Definition at line 855 of file SimParameters.h.

◆ PMESendOrder

int SimParameters::PMESendOrder

Definition at line 865 of file SimParameters.h.

◆ PMETolerance

BigReal SimParameters::PMETolerance

Definition at line 848 of file SimParameters.h.

◆ pressureProfileAtomTypes

int SimParameters::pressureProfileAtomTypes

Definition at line 771 of file SimParameters.h.

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

◆ pressureProfileEwaldOn

Bool SimParameters::pressureProfileEwaldOn

Definition at line 772 of file SimParameters.h.

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

◆ pressureProfileEwaldX

int SimParameters::pressureProfileEwaldX

Definition at line 773 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

◆ pressureProfileEwaldY

int SimParameters::pressureProfileEwaldY

Definition at line 774 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

◆ pressureProfileEwaldZ

int SimParameters::pressureProfileEwaldZ

Definition at line 775 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

◆ pressureProfileFreq

int SimParameters::pressureProfileFreq

Definition at line 770 of file SimParameters.h.

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

◆ pressureProfileOn

Bool SimParameters::pressureProfileOn

Definition at line 768 of file SimParameters.h.

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

◆ pressureProfileSlabs

int SimParameters::pressureProfileSlabs

Definition at line 769 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), Sequencer::Sequencer(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

◆ printBadContacts

Bool SimParameters::printBadContacts

Definition at line 559 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

◆ printExclusions

Bool SimParameters::printExclusions

Definition at line 1111 of file SimParameters.h.

◆ proxyRecvSpanningTree

int SimParameters::proxyRecvSpanningTree

Definition at line 1115 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

◆ proxySendSpanningTree

int SimParameters::proxySendSpanningTree

Definition at line 1114 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

◆ proxyTreeBranchFactor

int SimParameters::proxyTreeBranchFactor

Definition at line 1117 of file SimParameters.h.

Referenced by Node::startup().

◆ qmBaseDir

char SimParameters::qmBaseDir[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 515 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmBondColumn

char SimParameters::qmBondColumn[16]

Definition at line 525 of file SimParameters.h.

◆ qmBondColumnDefined

Bool SimParameters::qmBondColumnDefined

Definition at line 526 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmBondDist

Bool SimParameters::qmBondDist

Definition at line 527 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmBondGuess

Bool SimParameters::qmBondGuess

Definition at line 528 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmBondOn

Bool SimParameters::qmBondOn

Definition at line 524 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmBondScheme

int SimParameters::qmBondScheme

Definition at line 532 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmBondSchemeS

char SimParameters::qmBondSchemeS[16]

Definition at line 531 of file SimParameters.h.

◆ qmBondValType

int SimParameters::qmBondValType

Definition at line 529 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

◆ qmBondValueTypeS

char SimParameters::qmBondValueTypeS[16]

Definition at line 530 of file SimParameters.h.

◆ qmChrgFromPSF

Bool SimParameters::qmChrgFromPSF

Definition at line 509 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmChrgMode

int SimParameters::qmChrgMode

Definition at line 513 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmChrgModeS

char SimParameters::qmChrgModeS[16]

Definition at line 512 of file SimParameters.h.

◆ qmColumn

char SimParameters::qmColumn[16]

Definition at line 514 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmCSMD

Bool SimParameters::qmCSMD

Definition at line 552 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmCSMDFile

char SimParameters::qmCSMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 553 of file SimParameters.h.

◆ qmCustomPCSel

Bool SimParameters::qmCustomPCSel

Definition at line 544 of file SimParameters.h.

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

◆ qmElecEmbed

Bool SimParameters::qmElecEmbed

Definition at line 542 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmEnergyOutFreq

int SimParameters::qmEnergyOutFreq

Definition at line 555 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

◆ qmExecPath

char SimParameters::qmExecPath[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 510 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmForcesOn

Bool SimParameters::qmForcesOn

Definition at line 506 of file SimParameters.h.

Referenced by Controller::compareChecksums(), NamdState::loadStructure(), WorkDistrib::mapComputes(), and Controller::printEnergies().

◆ qmFormat

int SimParameters::qmFormat

Definition at line 520 of file SimParameters.h.

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

◆ qmLSSFreq

int SimParameters::qmLSSFreq

Definition at line 547 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmLSSMode

int SimParameters::qmLSSMode

Definition at line 550 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmLSSModeS

char SimParameters::qmLSSModeS[16]

Definition at line 549 of file SimParameters.h.

◆ qmLSSOn

Bool SimParameters::qmLSSOn

Definition at line 546 of file SimParameters.h.

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

◆ qmLSSResname

char SimParameters::qmLSSResname[5]

Definition at line 548 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmMOPACAddConfigChrg

Bool SimParameters::qmMOPACAddConfigChrg

Definition at line 522 of file SimParameters.h.

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

◆ qmNoPC

Bool SimParameters::qmNoPC

Definition at line 541 of file SimParameters.h.

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

◆ qmOutFreq

int SimParameters::qmOutFreq

Definition at line 556 of file SimParameters.h.

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

◆ qmParamPDB

char SimParameters::qmParamPDB[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 507 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ qmParamPDBDefined

Bool SimParameters::qmParamPDBDefined

Definition at line 508 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ qmPCScheme

int SimParameters::qmPCScheme

Definition at line 537 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmPCSchemeS

char SimParameters::qmPCSchemeS[16]

Definition at line 536 of file SimParameters.h.

◆ qmPCSelFreq

int SimParameters::qmPCSelFreq

Definition at line 543 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ qmPCSwitchOn

Bool SimParameters::qmPCSwitchOn

Definition at line 533 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmPCSwitchType

int SimParameters::qmPCSwitchType

Definition at line 535 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmPCSwitchTypeS

char SimParameters::qmPCSwitchTypeS[16]

Definition at line 534 of file SimParameters.h.

◆ qmPosOutFreq

int SimParameters::qmPosOutFreq

Definition at line 557 of file SimParameters.h.

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

◆ qmPrepProc

char SimParameters::qmPrepProc[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 518 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmPrepProcOn

Bool SimParameters::qmPrepProcOn

Definition at line 519 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmReplaceAll

Bool SimParameters::qmReplaceAll

Definition at line 521 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ qmSecProc

char SimParameters::qmSecProc[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 516 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmSecProcOn

Bool SimParameters::qmSecProcOn

Definition at line 517 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ qmSimsPerNode

int SimParameters::qmSimsPerNode

Definition at line 538 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

◆ qmSoftware

char SimParameters::qmSoftware[128]

Definition at line 511 of file SimParameters.h.

◆ qmVDW

Bool SimParameters::qmVDW

Definition at line 540 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

◆ randomSeed

unsigned int SimParameters::randomSeed

Definition at line 780 of file SimParameters.h.

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

◆ readExclusions

Bool SimParameters::readExclusions

Definition at line 1085 of file SimParameters.h.

Referenced by buildExclusions().

◆ reassignFreq

int SimParameters::reassignFreq

Definition at line 716 of file SimParameters.h.

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

◆ reassignHold

BigReal SimParameters::reassignHold

Definition at line 719 of file SimParameters.h.

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

◆ reassignIncr

BigReal SimParameters::reassignIncr

Definition at line 718 of file SimParameters.h.

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

◆ reassignTemp

BigReal SimParameters::reassignTemp

Definition at line 717 of file SimParameters.h.

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

◆ replicaUniformPatchGrids

Bool SimParameters::replicaUniformPatchGrids

Definition at line 1044 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ rescaleFreq

int SimParameters::rescaleFreq

Definition at line 667 of file SimParameters.h.

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

◆ rescaleTemp

BigReal SimParameters::rescaleTemp

Definition at line 668 of file SimParameters.h.

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

◆ restartFilename

char SimParameters::restartFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 254 of file SimParameters.h.

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

◆ restartFrequency

int SimParameters::restartFrequency

Definition at line 256 of file SimParameters.h.

Referenced by colvarproxy_namd::calculate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate_SOA(), Controller::outputExtendedSystem(), and Controller::rescaleaccelMD().

◆ restartSave

Bool SimParameters::restartSave

Definition at line 258 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

◆ restartSaveDcd

Bool SimParameters::restartSaveDcd

Definition at line 259 of file SimParameters.h.

◆ rigidBonds

int SimParameters::rigidBonds

Definition at line 1010 of file SimParameters.h.

Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), outputCompressedFile(), Sequencer::rattle1(), and Sequencer::rattle1_SOA().

◆ rigidDie

int SimParameters::rigidDie

Definition at line 1015 of file SimParameters.h.

◆ rigidIter

int SimParameters::rigidIter

Definition at line 1014 of file SimParameters.h.

◆ rigidTol

BigReal SimParameters::rigidTol

Definition at line 1013 of file SimParameters.h.

◆ rotConsAxis

zVector SimParameters::rotConsAxis

Definition at line 354 of file SimParameters.h.

◆ rotConsPivot

zVector SimParameters::rotConsPivot

Definition at line 355 of file SimParameters.h.

◆ rotConstraintsOn

Bool SimParameters::rotConstraintsOn

Definition at line 352 of file SimParameters.h.

◆ rotConsVel

BigReal SimParameters::rotConsVel

Definition at line 356 of file SimParameters.h.

◆ rotDragAxisFile

char SimParameters::rotDragAxisFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 371 of file SimParameters.h.

◆ rotDragFile

char SimParameters::rotDragFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 369 of file SimParameters.h.

◆ rotDragGlobVel

BigReal SimParameters::rotDragGlobVel

Definition at line 373 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

◆ rotDragOn

Bool SimParameters::rotDragOn

Definition at line 368 of file SimParameters.h.

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

◆ rotDragPivotFile

char SimParameters::rotDragPivotFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 372 of file SimParameters.h.

◆ rotDragVelFile

char SimParameters::rotDragVelFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 374 of file SimParameters.h.

◆ scale14

BigReal SimParameters::scale14

Definition at line 227 of file SimParameters.h.

◆ scale14alt

BigReal SimParameters::scale14alt

Definition at line 229 of file SimParameters.h.

◆ scriptArg1

BigReal SimParameters::scriptArg1

Definition at line 1095 of file SimParameters.h.

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

◆ scriptArg2

BigReal SimParameters::scriptArg2

Definition at line 1096 of file SimParameters.h.

◆ scriptArg3

BigReal SimParameters::scriptArg3

Definition at line 1097 of file SimParameters.h.

◆ scriptArg4

BigReal SimParameters::scriptArg4

Definition at line 1098 of file SimParameters.h.

◆ scriptArg5

BigReal SimParameters::scriptArg5

Definition at line 1099 of file SimParameters.h.

◆ scriptIntArg1

int SimParameters::scriptIntArg1

Definition at line 1100 of file SimParameters.h.

Referenced by Controller::algorithm().

◆ scriptIntArg2

int SimParameters::scriptIntArg2

Definition at line 1101 of file SimParameters.h.

◆ scriptStringArg1

char SimParameters::scriptStringArg1[128]

Definition at line 1102 of file SimParameters.h.

Referenced by Controller::algorithm().

◆ scriptStringArg2

char SimParameters::scriptStringArg2[128]

Definition at line 1103 of file SimParameters.h.

◆ sdScaling

Bool SimParameters::sdScaling

Definition at line 431 of file SimParameters.h.

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

◆ selectConstraintsOn

Bool SimParameters::selectConstraintsOn

Definition at line 319 of file SimParameters.h.

◆ simulatedNodeSize

int SimParameters::simulatedNodeSize

Definition at line 189 of file SimParameters.h.

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

◆ simulatedPEs

int SimParameters::simulatedPEs

Definition at line 188 of file SimParameters.h.

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

◆ simulateInitialMapping

Bool SimParameters::simulateInitialMapping

Definition at line 187 of file SimParameters.h.

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

◆ singleTopology

Bool SimParameters::singleTopology

Definition at line 430 of file SimParameters.h.

Referenced by Sequencer::integrate(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::minimize(), and Sequencer::runComputeObjects().

◆ SMDDir

zVector SimParameters::SMDDir

Definition at line 391 of file SimParameters.h.

◆ SMDFile

char SimParameters::SMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 394 of file SimParameters.h.

◆ SMDk

BigReal SimParameters::SMDk

Definition at line 392 of file SimParameters.h.

◆ SMDk2

BigReal SimParameters::SMDk2

Definition at line 393 of file SimParameters.h.

◆ SMDOn

Bool SimParameters::SMDOn

Definition at line 389 of file SimParameters.h.

◆ SMDOutputFreq

int SimParameters::SMDOutputFreq

Definition at line 395 of file SimParameters.h.

◆ SMDVel

BigReal SimParameters::SMDVel

Definition at line 390 of file SimParameters.h.

◆ SOAintegrateOn

Bool SimParameters::SOAintegrateOn

Definition at line 124 of file SimParameters.h.

Referenced by Sequencer::algorithm(), ComputeGlobal::ComputeGlobal(), ComputeGlobal::doWork(), ComputeGlobal::recvResults(), Sequencer::rescaleSoluteCharges(), and ComputeGlobal::saveTotalForces().

◆ soluteScalingAll

Bool SimParameters::soluteScalingAll

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

Definition at line 496 of file SimParameters.h.

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

◆ soluteScalingFactor

BigReal SimParameters::soluteScalingFactor

scaling factor for solute interactions

Definition at line 488 of file SimParameters.h.

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

◆ soluteScalingFactorCharge

BigReal SimParameters::soluteScalingFactorCharge

optional independent control over scaling factor for electrostatic interactions of solute

Definition at line 490 of file SimParameters.h.

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

◆ soluteScalingFactorVdw

BigReal SimParameters::soluteScalingFactorVdw

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

Definition at line 493 of file SimParameters.h.

◆ soluteScalingOn

Bool SimParameters::soluteScalingOn

REST2 (replica exchange solute tempering) on?

Definition at line 486 of file SimParameters.h.

Referenced by LJTable::LJTable(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and Sequencer::Sequencer().

◆ solvent_dielectric

BigReal SimParameters::solvent_dielectric

Definition at line 565 of file SimParameters.h.

◆ sphericalBCexp1

int SimParameters::sphericalBCexp1

Definition at line 925 of file SimParameters.h.

◆ sphericalBCexp2

int SimParameters::sphericalBCexp2

Definition at line 926 of file SimParameters.h.

◆ sphericalBCk1

BigReal SimParameters::sphericalBCk1

Definition at line 919 of file SimParameters.h.

◆ sphericalBCk2

BigReal SimParameters::sphericalBCk2

Definition at line 921 of file SimParameters.h.

◆ sphericalBCOn

Bool SimParameters::sphericalBCOn

Definition at line 916 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ sphericalBCr1

BigReal SimParameters::sphericalBCr1

Definition at line 923 of file SimParameters.h.

◆ sphericalBCr2

BigReal SimParameters::sphericalBCr2

Definition at line 924 of file SimParameters.h.

◆ sphericalCenter

zVector SimParameters::sphericalCenter

Definition at line 918 of file SimParameters.h.

◆ sphericalConstraintsOn

Bool SimParameters::sphericalConstraintsOn

Definition at line 327 of file SimParameters.h.

◆ sphericalConstrCenter

zVector SimParameters::sphericalConstrCenter

Definition at line 328 of file SimParameters.h.

◆ splitPatch

int SimParameters::splitPatch

Definition at line 1003 of file SimParameters.h.

◆ staticAtomAssignment

Bool SimParameters::staticAtomAssignment

Definition at line 1043 of file SimParameters.h.

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

◆ statsOn

Bool SimParameters::statsOn

Definition at line 1021 of file SimParameters.h.

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

◆ stepsPerCycle

int SimParameters::stepsPerCycle

Definition at line 149 of file SimParameters.h.

Referenced by Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::minimize(), Sequencer::multigratorPressure(), Molecule::prepare_qm(), and Sequencer::Sequencer().

◆ stirAxis

zVector SimParameters::stirAxis

Definition at line 953 of file SimParameters.h.

◆ stirFilename

char SimParameters::stirFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 948 of file SimParameters.h.

◆ stirK

BigReal SimParameters::stirK

Definition at line 952 of file SimParameters.h.

◆ stirOn

Bool SimParameters::stirOn

Definition at line 947 of file SimParameters.h.

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

◆ stirPivot

zVector SimParameters::stirPivot

Definition at line 954 of file SimParameters.h.

◆ stirStartingTheta

BigReal SimParameters::stirStartingTheta

Definition at line 950 of file SimParameters.h.

◆ stirVel

BigReal SimParameters::stirVel

Definition at line 951 of file SimParameters.h.

◆ stochRescaleFreq

int SimParameters::stochRescaleFreq

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 659 of file SimParameters.h.

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

◆ stochRescaleHeat

Bool SimParameters::stochRescaleHeat

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

Definition at line 662 of file SimParameters.h.

Referenced by Controller::printEnergies().

◆ stochRescaleOn

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 646 of file SimParameters.h.

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

◆ stochRescalePeriod

BigReal SimParameters::stochRescalePeriod

Timescale (ps) for stochastic velocity rescaling.

Definition at line 656 of file SimParameters.h.

Referenced by Controller::Controller().

◆ stochRescaleTemp

BigReal SimParameters::stochRescaleTemp

Temperature for stochastic velocity rescaling.

Definition at line 653 of file SimParameters.h.

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

◆ storeComputeMap

Bool SimParameters::storeComputeMap

Definition at line 1132 of file SimParameters.h.

◆ strainRate

zVector SimParameters::strainRate

Definition at line 777 of file SimParameters.h.

Referenced by Controller::Controller().

◆ strainRate2

zVector SimParameters::strainRate2

Definition at line 778 of file SimParameters.h.

Referenced by Controller::Controller().

◆ surface_tension

BigReal SimParameters::surface_tension

Definition at line 575 of file SimParameters.h.

◆ surfaceTensionTarget

BigReal SimParameters::surfaceTensionTarget

Definition at line 766 of file SimParameters.h.

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

◆ switchingActive

Bool SimParameters::switchingActive

Definition at line 273 of file SimParameters.h.

◆ switchingDist

BigReal SimParameters::switchingDist

Definition at line 277 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

◆ symmetryFile

char SimParameters::symmetryFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 419 of file SimParameters.h.

◆ symmetryFirstFullStep

int SimParameters::symmetryFirstFullStep

Definition at line 421 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

◆ symmetryFirstStep

int SimParameters::symmetryFirstStep

Definition at line 421 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

◆ symmetryk

BigReal SimParameters::symmetryk

Definition at line 417 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

◆ symmetrykfile

char SimParameters::symmetrykfile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 418 of file SimParameters.h.

◆ symmetryLastFullStep

int SimParameters::symmetryLastFullStep

Definition at line 421 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

◆ symmetryLastStep

int SimParameters::symmetryLastStep

Definition at line 421 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

◆ symmetryMatrixFile

char SimParameters::symmetryMatrixFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 420 of file SimParameters.h.

◆ symmetryOn

Bool SimParameters::symmetryOn

Definition at line 416 of file SimParameters.h.

◆ symmetryScaleForces

Bool SimParameters::symmetryScaleForces

Definition at line 416 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

◆ tableInterpType

char SimParameters::tableInterpType[128]

Definition at line 402 of file SimParameters.h.

◆ tableMaxDist

BigReal SimParameters::tableMaxDist

Definition at line 404 of file SimParameters.h.

◆ tableNumTypes

int SimParameters::tableNumTypes

Definition at line 400 of file SimParameters.h.

◆ tableSpacing

Real SimParameters::tableSpacing

Definition at line 403 of file SimParameters.h.

◆ tabulatedEnergies

Bool SimParameters::tabulatedEnergies

Definition at line 399 of file SimParameters.h.

◆ tabulatedEnergiesFile

char SimParameters::tabulatedEnergiesFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 401 of file SimParameters.h.

◆ tclBCArgs

char SimParameters::tclBCArgs[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 607 of file SimParameters.h.

◆ tclBCOn

Bool SimParameters::tclBCOn

Definition at line 605 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ tclBCScript

char* SimParameters::tclBCScript

Definition at line 606 of file SimParameters.h.

◆ tclForcesOn

Bool SimParameters::tclForcesOn

Definition at line 594 of file SimParameters.h.

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

◆ tclIsThreaded

Bool SimParameters::tclIsThreaded

Definition at line 603 of file SimParameters.h.

◆ tCoupleOn

Bool SimParameters::tCoupleOn

Definition at line 642 of file SimParameters.h.

Referenced by NamdState::loadStructure(), Controller::tcoupleVelocities(), Sequencer::tcoupleVelocities(), and colvarproxy_namd::update_target_temperature().

◆ tCoupleTemp

BigReal SimParameters::tCoupleTemp

Definition at line 644 of file SimParameters.h.

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

◆ testOn

Bool SimParameters::testOn

Definition at line 1019 of file SimParameters.h.

◆ TMDDiffRMSD

Bool SimParameters::TMDDiffRMSD

Definition at line 408 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDFile

char SimParameters::TMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 410 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDFile2

char SimParameters::TMDFile2[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 410 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDFinalRMSD

BigReal SimParameters::TMDFinalRMSD

Definition at line 413 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDFirstStep

int SimParameters::TMDFirstStep

Definition at line 412 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDInitialRMSD

BigReal SimParameters::TMDInitialRMSD

Definition at line 413 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDk

BigReal SimParameters::TMDk

Definition at line 409 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDLastStep

int SimParameters::TMDLastStep

Definition at line 412 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ TMDOn

Bool SimParameters::TMDOn

Definition at line 408 of file SimParameters.h.

◆ TMDOutputFreq

int SimParameters::TMDOutputFreq

Definition at line 411 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

◆ totalAtoms

int SimParameters::totalAtoms

Definition at line 1023 of file SimParameters.h.

◆ traceStartStep

int SimParameters::traceStartStep

Definition at line 177 of file SimParameters.h.

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

◆ twoAwayX

int SimParameters::twoAwayX

Definition at line 201 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ twoAwayY

int SimParameters::twoAwayY

Definition at line 202 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ twoAwayZ

int SimParameters::twoAwayZ

Definition at line 203 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

◆ updateAtomMap

Bool SimParameters::updateAtomMap

Used for experimenting with atom maps

Definition at line 895 of file SimParameters.h.

◆ useAntecedent

Bool SimParameters::useAntecedent

Definition at line 1055 of file SimParameters.h.

◆ useAVXTiles

Bool SimParameters::useAVXTiles

Definition at line 1145 of file SimParameters.h.

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

◆ useCkLoop

int SimParameters::useCkLoop

Definition at line 199 of file SimParameters.h.

Referenced by PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), 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().

◆ useCompressedPsf

Bool SimParameters::useCompressedPsf

Definition at line 1105 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ useConstantArea

Bool SimParameters::useConstantArea

Definition at line 727 of file SimParameters.h.

Referenced by Controller::langevinPiston1(), Controller::monteCarloPressure_accept(), and Controller::monteCarloPressure_prepare().

◆ useConstantRatio

Bool SimParameters::useConstantRatio

Definition at line 728 of file SimParameters.h.

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

◆ useCUDAdisable

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 882 of file SimParameters.h.

◆ useCudaGlobal

Bool SimParameters::useCudaGlobal

Definition at line 1147 of file SimParameters.h.

◆ useCUDANonbondedForceTable

Bool SimParameters::useCUDANonbondedForceTable

direct nonbonded kernel math for non-PME steps (experimental)

Definition at line 890 of file SimParameters.h.

◆ useDeviceMigration

Bool SimParameters::useDeviceMigration

atom migration on GPU (experimental)

Definition at line 893 of file SimParameters.h.

Referenced by Sequencer::minimize(), CudaComputeNonbonded::patchReady(), and Sequencer::submitCollections_SOA().

◆ useDPME

Bool SimParameters::useDPME

Definition at line 868 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

◆ useFlexibleCell

Bool SimParameters::useFlexibleCell

Definition at line 726 of file SimParameters.h.

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

◆ useGPUAtomMigration

Bool SimParameters::useGPUAtomMigration

replacement for useDeviceMigration

Definition at line 894 of file SimParameters.h.

◆ useGPUNonbondedForceTable

Bool SimParameters::useGPUNonbondedForceTable

replacement for useCUDANonbondedForceTable

Definition at line 891 of file SimParameters.h.

◆ useGroupPressure

Bool SimParameters::useGroupPressure

Definition at line 721 of file SimParameters.h.

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

◆ usePairlists

int SimParameters::usePairlists

Definition at line 287 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects(), and Sequencer::runComputeObjects_SOA().

◆ usePluginIO

Bool SimParameters::usePluginIO

Definition at line 1108 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ usePMECUDA

Bool SimParameters::usePMECUDA

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

Definition at line 870 of file SimParameters.h.

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

◆ usePMEGPU

Bool SimParameters::usePMEGPU

replacement keyword for usePMECUDA

Definition at line 873 of file SimParameters.h.

◆ usePytorchForces

Bool SimParameters::usePytorchForces

Definition at line 1149 of file SimParameters.h.

◆ useSettle

Bool SimParameters::useSettle

Definition at line 1017 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

◆ vdwForceSwitching

Bool SimParameters::vdwForceSwitching

Definition at line 275 of file SimParameters.h.

◆ vdwGeometricSigma

Bool SimParameters::vdwGeometricSigma

Definition at line 1092 of file SimParameters.h.

◆ vdwscale14

BigReal SimParameters::vdwscale14

Definition at line 1086 of file SimParameters.h.

Referenced by NamdState::loadStructure().

◆ velDcdFilename

char SimParameters::velDcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 246 of file SimParameters.h.

◆ velDcdFrequency

int SimParameters::velDcdFrequency

Definition at line 237 of file SimParameters.h.

Referenced by Sequencer::integrate_SOA().

◆ verboseTopology

Bool SimParameters::verboseTopology

Definition at line 191 of file SimParameters.h.

◆ watmodel

WaterModel SimParameters::watmodel

Definition at line 143 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), and Sequencer::runComputeObjects().

◆ wrapAll

Bool SimParameters::wrapAll

Definition at line 220 of file SimParameters.h.

Referenced by colvarproxy_namd::setup().

◆ wrapNearest

Bool SimParameters::wrapNearest

Definition at line 221 of file SimParameters.h.

◆ wrapWater

Bool SimParameters::wrapWater

Definition at line 219 of file SimParameters.h.

◆ xstFilename

char SimParameters::xstFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 248 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

◆ xstFrequency

int SimParameters::xstFrequency

Definition at line 241 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

◆ zeroMomentum

Bool SimParameters::zeroMomentum

Definition at line 217 of file SimParameters.h.

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

◆ zeroMomentumAlt

Bool SimParameters::zeroMomentumAlt

Definition at line 218 of file SimParameters.h.

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

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

Public Member Functions

Static Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SimParameters() [1/2]

◆ SimParameters() [2/2]

◆ ~SimParameters()

Member Function Documentation

◆ alchGetNumOfPMEGrids()

◆ close_dcdfile()

◆ close_veldcdfile()

◆ getBondLambda()

◆ getCurrentLambda()

◆ getCurrentLambda2()

◆ getElecLambda()

◆ getfromparseopts()

◆ getLambdaDelta()

◆ getRepLambda()

◆ getVdwLambda()

◆ initialize_config_data()

◆ isMultiTimeStepping()

◆ isRecvSpanningTreeOn()

◆ isRecvSpanningTreeUnset()

◆ isSendSpanningTreeOn()

◆ isSendSpanningTreeUnset()

◆ issetinparseopts()

◆ istrueinparseopts()

◆ nonbonded_select()

◆ pme_select()

◆ readExtendedSystem()

◆ receive_SimParameters()

◆ scriptSet()

◆ send_SimParameters()

◆ setupIDWS()

Member Data Documentation

◆ aaAngleExp

◆ accelMDalpha

◆ accelMDDebugOn

◆ accelMDdihe

◆ accelMDdual

◆ accelMDE

◆ accelMDFirstStep

◆ accelMDG

◆ accelMDGcMDPrepSteps

◆ accelMDGcMDSteps

◆ accelMDGEquiPrepSteps

◆ accelMDGEquiSteps

◆ accelMDGiE

◆ accelMDGresetVaftercmd

◆ accelMDGRestart

◆ accelMDGRestartFile

◆ accelMDGSigma0D

◆ accelMDGSigma0P

◆ accelMDGStatWindow

◆ accelMDLastStep

◆ accelMDOn

◆ accelMDOutFreq

◆ accelMDTalpha

◆ accelMDTE

◆ adaptTempAutoDt

◆ adaptTempBins

◆ adaptTempCgamma

◆ adaptTempDebug

◆ adaptTempDt

◆ adaptTempFirstStep

◆ adaptTempFreq

◆ adaptTempInFile

◆ adaptTempLangevin

◆ adaptTempLastStep

◆ adaptTempOn

◆ adaptTempOutFreq

◆ adaptTempRandom

◆ adaptTempRescale

◆ adaptTempRestartFile

◆ adaptTempRestartFreq

◆ adaptTempTmax

◆ adaptTempTmin

◆ alchBondDecouple

◆ alchBondLambdaEnd