#include <SimParameters.h>

Public Member Functions
BigReal	getCurrentLambda (const int)

BigReal	getCurrentLambda2 (const int)

int	setupIDWS ()

BigReal	getLambdaDelta (void)

BigReal	getElecLambda (const BigReal)

BigReal	getVdwLambda (const BigReal)

BigReal	getRepLambda (const BigReal)

BigReal	getBondLambda (const BigReal)

	SimParameters ()

	SimParameters (ConfigList c, char &cwd)

	~SimParameters ()

void	initialize_config_data (ConfigList , char &cwd)

void	send_SimParameters (MOStream *)

void	receive_SimParameters (MIStream *)

void	scriptSet (const char , const char )

void	close_dcdfile ()

void	close_veldcdfile ()

int	isSendSpanningTreeOn ()

int	isSendSpanningTreeUnset ()

int	isRecvSpanningTreeOn ()

int	isRecvSpanningTreeUnset ()

char *	getfromparseopts (const char name, char outbuf)

int	istrueinparseopts (const char *name)

int	issetinparseopts (const char *name)

void	readExtendedSystem (const char filename, Lattice latptr=0)

Static Public Member Functions
static void	nonbonded_select ()

static void	pme_select ()

Public Attributes
Bool	lonepairs

int	watmodel

Bool	LJcorrection

BigReal	dt

int	N

int	stepsPerCycle

zVector	cellBasisVector1

zVector	cellBasisVector2

zVector	cellBasisVector3

zVector	cellOrigin

Lattice	lattice

int	nonbondedFrequency

int	fullElectFrequency

BigReal	fmaTheta

int	ldBalancer

int	ldbStrategy

int	ldbPeriod

int	firstLdbStep

int	lastLdbStep

int	hybridGroupSize

BigReal	ldbBackgroundScaling

BigReal	ldbPMEBackgroundScaling

BigReal	ldbHomeBackgroundScaling

BigReal	ldbRelativeGrainsize

int	traceStartStep

int	numTraceSteps

Bool	outputMaps

Bool	simulateInitialMapping

int	simulatedPEs

int	simulatedNodeSize

Bool	disableTopology

Bool	verboseTopology

Bool	benchTimestep

int	useCkLoop

int	twoAwayX

int	twoAwayY

int	twoAwayZ

int	maxPatches

Bool	ldbUnloadPME

Bool	ldbUnloadZero

Bool	ldbUnloadOne

Bool	ldbUnloadOutputPEs

Bool	noPatchesOnZero

Bool	noPatchesOnOutputPEs

Bool	noPatchesOnOne

BigReal	initialTemp

Bool	comMove

Bool	zeroMomentum

Bool	zeroMomentumAlt

Bool	wrapWater

Bool	wrapAll

Bool	wrapNearest

BigReal	dielectric

ExclusionSettings	exclude

BigReal	scale14

BigReal	nonbondedScaling

int	dcdFrequency

int	dcdUnitCell

int	velDcdFrequency

int	forceDcdFrequency

int	xstFrequency

char	auxFilename [NAMD_FILENAME_BUFFER_SIZE]

char	dcdFilename [NAMD_FILENAME_BUFFER_SIZE]

char	velDcdFilename [NAMD_FILENAME_BUFFER_SIZE]

char	forceDcdFilename [NAMD_FILENAME_BUFFER_SIZE]

char	xstFilename [NAMD_FILENAME_BUFFER_SIZE]

char	outputFilename [NAMD_FILENAME_BUFFER_SIZE]

char	restartFilename [NAMD_FILENAME_BUFFER_SIZE]

int	restartFrequency

Bool	restartSave

Bool	restartSaveDcd

Bool	binaryRestart

Bool	binaryOutput

BigReal	cutoff

BigReal	margin

BigReal	patchDimension

BigReal	limitDist

Bool	switchingActive

Bool	vdwForceSwitching

BigReal	switchingDist

Bool	martiniSwitching

Bool	martiniDielAllow

BigReal	pairlistDist

int	pairlistMinProcs

int	usePairlists

int	pairlistsPerCycle

BigReal	pairlistShrink

BigReal	pairlistGrow

BigReal	pairlistTrigger

int	outputPairlists

Bool	constraintsOn

int	constraintExp

Bool	gridforceOn

Bool	gridforceVolts

zVector	gridforceScale

Bool	gridforceContA1

Bool	gridforceContA2

Bool	gridforceContA3

zVector	gridforceVOffset

Bool	gridforceLite

Bool	gridforcechecksize

Bool	mgridforceOn

MGridforceParamsList	mgridforcelist

Bool	selectConstraintsOn

Bool	constrXOn

Bool	constrYOn

Bool	constrZOn

Bool	sphericalConstraintsOn

zVector	sphericalConstrCenter

BigReal	constraintScaling

Bool	paraTypeXplorOn

Bool	paraTypeCharmmOn

Bool	goGroPair

Bool	goForcesOn

char	goParameters [NAMD_FILENAME_BUFFER_SIZE]

char	goCoordinates [NAMD_FILENAME_BUFFER_SIZE]

GoChoices	goMethod

Bool	movingConstraintsOn

zVector	movingConsVel

Bool	rotConstraintsOn

zVector	rotConsAxis

zVector	rotConsPivot

BigReal	rotConsVel

Bool	movDragOn

char	movDragFile [NAMD_FILENAME_BUFFER_SIZE]

BigReal	movDragGlobVel

char	movDragVelFile [NAMD_FILENAME_BUFFER_SIZE]

Bool	rotDragOn

char	rotDragFile [NAMD_FILENAME_BUFFER_SIZE]

char	rotDragAxisFile [NAMD_FILENAME_BUFFER_SIZE]

char	rotDragPivotFile [NAMD_FILENAME_BUFFER_SIZE]

BigReal	rotDragGlobVel

char	rotDragVelFile [NAMD_FILENAME_BUFFER_SIZE]

Bool	consTorqueOn

char	consTorqueFile [NAMD_FILENAME_BUFFER_SIZE]

char	consTorqueAxisFile [NAMD_FILENAME_BUFFER_SIZE]

char	consTorquePivotFile [NAMD_FILENAME_BUFFER_SIZE]

BigReal	consTorqueGlobVal

char	consTorqueValFile [NAMD_FILENAME_BUFFER_SIZE]

Bool	SMDOn

BigReal	SMDVel

zVector	SMDDir

BigReal	SMDk

BigReal	SMDk2

char	SMDFile [NAMD_FILENAME_BUFFER_SIZE]

int	SMDOutputFreq

Bool	tabulatedEnergies

int	tableNumTypes

char	tabulatedEnergiesFile [NAMD_FILENAME_BUFFER_SIZE]

char	tableInterpType [128]

Real	tableSpacing

BigReal	tableMaxDist

Bool	TMDOn

Bool	TMDDiffRMSD

BigReal	TMDk

char	TMDFile [NAMD_FILENAME_BUFFER_SIZE]

char	TMDFile2 [NAMD_FILENAME_BUFFER_SIZE]

int	TMDOutputFreq

int	TMDFirstStep

int	TMDLastStep

BigReal	TMDInitialRMSD

BigReal	TMDFinalRMSD

Bool	symmetryOn

Bool	symmetryScaleForces

BigReal	symmetryk

char	symmetrykfile [NAMD_FILENAME_BUFFER_SIZE]

char	symmetryFile [NAMD_FILENAME_BUFFER_SIZE]

char	symmetryMatrixFile [NAMD_FILENAME_BUFFER_SIZE]

int	symmetryFirstStep

int	symmetryLastStep

int	symmetryFirstFullStep

int	symmetryLastFullStep

Bool	alchOnAtStartup

Bool	alchFepOnAtStartup

Bool	alchThermIntOnAtStartup

Bool	alchOn

Bool	alchFepOn

Bool	singleTopology

Bool	sdScaling

Bool	alchThermIntOn

Bool	alchWCAOn

int	alchMethod

BigReal	alchLambda

BigReal	alchLambda2

BigReal	alchLambdaIDWS

int	alchIDWSFreq

int	alchLambdaFreq

BigReal	alchTemp

int	alchOutFreq

Bool	alchEnsembleAvg

char	alchOutFile [NAMD_FILENAME_BUFFER_SIZE]

int	alchEquilSteps

BigReal	alchVdwShiftCoeff

BigReal	alchElecLambdaStart

BigReal	alchVdwLambdaEnd

BigReal	alchRepLambdaEnd

BigReal	alchBondLambdaEnd

Bool	alchDecouple

Bool	alchBondDecouple

Bool	lesOn

int	lesFactor

Bool	lesReduceTemp

Bool	lesReduceMass

Bool	soluteScalingOn

BigReal	soluteScalingFactor

BigReal	soluteScalingFactorCharge

BigReal	soluteScalingFactorVdw

Bool	soluteScalingAll

Bool	extForcesOn

char	extForcesCommand [NAMD_FILENAME_BUFFER_SIZE]

char	extCoordFilename [NAMD_FILENAME_BUFFER_SIZE]

char	extForceFilename [NAMD_FILENAME_BUFFER_SIZE]

Bool	qmForcesOn

char	qmParamPDB [NAMD_FILENAME_BUFFER_SIZE]

Bool	qmParamPDBDefined

Bool	qmChrgFromPSF

char	qmExecPath [NAMD_FILENAME_BUFFER_SIZE]

char	qmSoftware [128]

char	qmChrgModeS [16]

int	qmChrgMode

char	qmColumn [16]

char	qmBaseDir [NAMD_FILENAME_BUFFER_SIZE]

char	qmSecProc [NAMD_FILENAME_BUFFER_SIZE]

Bool	qmSecProcOn

char	qmPrepProc [NAMD_FILENAME_BUFFER_SIZE]

Bool	qmPrepProcOn

int	qmFormat

Bool	qmReplaceAll

Bool	qmMOPACAddConfigChrg

Bool	qmBondOn

char	qmBondColumn [16]

Bool	qmBondDist

int	qmBondValType

char	qmBondValueTypeS [16]

char	qmBondSchemeS [16]

int	qmBondScheme

Bool	qmPCSwitchOn

char	qmPCSwitchTypeS [16]

int	qmPCSwitchType

char	qmPCSchemeS [16]

int	qmPCScheme

int	qmSimsPerNode

Bool	qmVDW

Bool	qmNoPC

Bool	qmElecEmbed

int	qmPCSelFreq

Bool	qmCustomPCSel

Bool	qmLSSOn

int	qmLSSFreq

char	qmLSSResname [5]

char	qmLSSModeS [16]

int	qmLSSMode

Bool	qmCSMD

char	qmCSMDFile [NAMD_FILENAME_BUFFER_SIZE]

int	qmEnergyOutFreq

int	qmOutFreq

int	qmPosOutFreq

Bool	printBadContacts

Bool	GBISOn

BigReal	fsMax

Bool	GBISserOn

BigReal	solvent_dielectric

BigReal	coulomb_radius_offset

BigReal	kappa

BigReal	ion_concentration

BigReal	gbis_delta

BigReal	gbis_beta

BigReal	gbis_gamma

BigReal	alpha_cutoff

BigReal	alpha_max

Bool	LCPOOn

BigReal	surface_tension

Bool	drudeOn

Bool	drudeHardWallOn

BigReal	drudeTemp

BigReal	drudeDamping

BigReal	drudeBondLen

BigReal	drudeBondConst

BigReal	drudeNbtholeCut

Bool	pairInteractionOn

int	pairInteractionGroup1

int	pairInteractionGroup2

Bool	pairInteractionSelf

Bool	cosAngles

Bool	globalForcesOn

Bool	tclForcesOn

Bool	tclIsThreaded

Bool	tclBCOn

char *	tclBCScript

char	tclBCArgs [NAMD_FILENAME_BUFFER_SIZE]

Bool	freeEnergyOn

Bool	miscForcesOn

Bool	colvarsOn

Bool	fixedAtomsOn

Bool	fixedAtomsForces

Bool	fixedAtomsForceOutput

Bool	langevinOnAtStartup

Bool	langevinOn

BigReal	langevinTemp

BigReal	langevinDamping

Bool	langevinHydrogen

Bool	langevin_useBAOAB

Bool	loweAndersenOn

BigReal	loweAndersenTemp

BigReal	loweAndersenRate

BigReal	loweAndersenCutoff

Bool	globalOn

Bool	dihedralOn

Bool	COLDOn

BigReal	COLDRate

BigReal	COLDTemp

Bool	tCoupleOn

BigReal	tCoupleTemp

Bool	stochRescaleOn

BigReal	stochRescaleTemp

BigReal	stochRescalePeriod

int	stochRescaleFreq

Bool	stochRescaleHeat

int	rescaleFreq

BigReal	rescaleTemp

Bool	accelMDOn

Bool	accelMDdihe

Bool	accelMDdual

Bool	accelMDDebugOn

BigReal	accelMDFirstStep

BigReal	accelMDLastStep

int	accelMDOutFreq

BigReal	accelMDE

BigReal	accelMDalpha

BigReal	accelMDTE

BigReal	accelMDTalpha

Bool	accelMDG

int	accelMDGiE

int	accelMDGcMDSteps

int	accelMDGEquiSteps

int	accelMDGcMDPrepSteps

int	accelMDGEquiPrepSteps

int	accelMDGStatWindow

BigReal	accelMDGSigma0P

BigReal	accelMDGSigma0D

Bool	accelMDGRestart

char	accelMDGRestartFile [NAMD_FILENAME_BUFFER_SIZE]

Bool	accelMDGresetVaftercmd

Bool	adaptTempOn

Bool	adaptTempDebug

int	adaptTempFirstStep

int	adaptTempLastStep

int	adaptTempOutFreq

int	adaptTempFreq

BigReal	adaptTempTmin

BigReal	adaptTempTmax

BigReal	adaptTempAutoDt

int	adaptTempBins

BigReal	adaptTempDt

BigReal	adaptTempCgamma

Bool	adaptTempLangevin

Bool	adaptTempRescale

char	adaptTempInFile [NAMD_FILENAME_BUFFER_SIZE]

char	adaptTempRestartFile [NAMD_FILENAME_BUFFER_SIZE]

int	adaptTempRestartFreq

Bool	adaptTempRandom

int	reassignFreq

BigReal	reassignTemp

BigReal	reassignIncr

BigReal	reassignHold

Bool	useGroupPressure

Bool	excludeFromPressure

Bool	useFlexibleCell

Bool	useConstantArea

Bool	useConstantRatio

Bool	fixCellDims

Bool	fixCellDimX

Bool	fixCellDimY

Bool	fixCellDimZ

Bool	berendsenPressureOn

BigReal	berendsenPressureTarget

BigReal	berendsenPressureCompressibility

BigReal	berendsenPressureRelaxationTime

int	berendsenPressureFreq

Bool	langevinPistonOn

Bool	langevinPistonBarrier

BigReal	langevinPistonTarget

BigReal	langevinPistonPeriod

BigReal	langevinPistonDecay

BigReal	langevinPistonTemp

Bool	multigratorOn

BigReal	multigratorPressureTarget

BigReal	multigratorPressureRelaxationTime

int	multigratorPressureFreq

BigReal	multigratorTemperatureTarget

BigReal	multigratorTemperatureRelaxationTime

int	multigratorTemperatureFreq

int	multigratorNoseHooverChainLength

BigReal	surfaceTensionTarget

Bool	pressureProfileOn

int	pressureProfileSlabs

int	pressureProfileFreq

int	pressureProfileAtomTypes

Bool	pressureProfileEwaldOn

int	pressureProfileEwaldX

int	pressureProfileEwaldY

int	pressureProfileEwaldZ

zVector	strainRate

zVector	strainRate2

unsigned int	randomSeed

Bool	FMAOn

int	FMALevels

int	FMAMp

Bool	FMAFFTOn

int	FMAFFTBlock

Bool	fullDirectOn

Bool	MSMOn

int	MSMQuality

int	MSMApprox

int	MSMSplit

int	MSMLevels

int	MSMBlockSizeX

int	MSMBlockSizeY

int	MSMBlockSizeZ

BigReal	MSMGridSpacing

BigReal	MSMPadding

BigReal	MSMxmin

BigReal	MSMxmax

BigReal	MSMymin

BigReal	MSMymax

BigReal	MSMzmin

BigReal	MSMzmax

Bool	MsmSerialOn

Bool	FMMOn

int	FMMLevels

BigReal	FMMPadding

Bool	PMEOn

BigReal	PMETolerance

BigReal	PMEEwaldCoefficient

int	PMEInterpOrder

int	PMEGridSizeX

int	PMEGridSizeY

int	PMEGridSizeZ

BigReal	PMEGridSpacing

int	PMEProcessors

int	PMEMinSlices

int	PMEMinPoints

Bool	PMEBarrier

int	PMEPencils

int	PMEPencilsX

int	PMEPencilsY

int	PMEPencilsZ

int	PMEPencilsYLayout

int	PMEPencilsXLayout

int	PMESendOrder

Bool	PMEOffload

Bool	useDPME

Bool	usePMECUDA

Bool	useCUDA2

int	bondedCUDA

Bool	useCUDAdisable

Bool	FFTWEstimate

Bool	FFTWPatient

Bool	FFTWUseWisdom

char	FFTWWisdomFile [NAMD_FILENAME_BUFFER_SIZE]

char *	FFTWWisdomString

Bool	minimizeCGOn

Bool	minVerbose

BigReal	minTinyStep

BigReal	minBabyStep

BigReal	minLineGoal

Bool	minimizeOn

BigReal	maximumMove

Bool	sphericalBCOn

zVector	sphericalCenter

BigReal	sphericalBCk1

BigReal	sphericalBCk2

BigReal	sphericalBCr1

BigReal	sphericalBCr2

int	sphericalBCexp1

int	sphericalBCexp2

Bool	cylindricalBCOn

zVector	cylindricalCenter

char	cylindricalBCAxis

BigReal	cylindricalBCr1

BigReal	cylindricalBCr2

BigReal	cylindricalBCl1

BigReal	cylindricalBCl2

int	cylindricalBCexp1

int	cylindricalBCexp2

BigReal	cylindricalBCk1

BigReal	cylindricalBCk2

Bool	eFieldOn

Bool	eFieldNormalized

zVector	eField

BigReal	eFieldFreq

BigReal	eFieldPhase

Bool	stirOn

char	stirFilename [NAMD_FILENAME_BUFFER_SIZE]

BigReal	stirStartingTheta

BigReal	stirVel

BigReal	stirK

zVector	stirAxis

zVector	stirPivot

Bool	extraBondsOn

Bool	extraBondsCosAngles

Bool	extraBondsCosAnglesSetByUser

Bool	consForceOn

char	consForceFile [NAMD_FILENAME_BUFFER_SIZE]

BigReal	consForceScaling

int	outputEnergies

int	outputMomenta

int	outputTiming

int	outputCudaTiming

int	outputPressure

Bool	mergeCrossterms

int	firstTimestep

MTSChoices	MTSAlgorithm

int	longSplitting

Bool	ignoreMass

int	splitPatch

BigReal	hgroupCutoff

int	mollyOn

BigReal	mollyTol

int	mollyIter

int	rigidBonds

BigReal	rigidTol

int	rigidIter

int	rigidDie

Bool	useSettle

Bool	testOn

Bool	commOnly

Bool	statsOn

int	totalAtoms

int	maxSelfPart

int	maxPairPart

int	numAtomsSelf

int	numAtomsSelf2

int	numAtomsPair

int	numAtomsPair2

int	minAtomsPerPatch

int	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	readExclusions

BigReal	vdwscale14

Bool	gromacsOn

Bool	vdwGeometricSigma

BigReal	scriptArg1

BigReal	scriptArg2

BigReal	scriptArg3

BigReal	scriptArg4

BigReal	scriptArg5

int	scriptIntArg1

int	scriptIntArg2

char	scriptStringArg1 [128]

char	scriptStringArg2 [128]

Bool	useCompressedPsf

Bool	genCompressedPsf

Bool	usePluginIO

Bool	mallocTest

Bool	printExclusions

int	proxySendSpanningTree

int	proxyRecvSpanningTree

int	proxyTreeBranchFactor

int	numinputprocs

char *	binAtomFile

char *	binCoorFile

char *	binVelFile

char *	binRefFile

int	numoutputprocs

int	numoutputwrts

char	computeMapFilename [NAMD_FILENAME_BUFFER_SIZE]

Bool	storeComputeMap

Bool	loadComputeMap

int	mic_hostSplit

int	mic_numParts_self_p1

int	mic_numParts_pair_p1

int	mic_numParts_pair_p2

int	mic_unloadMICPEs

int	mic_deviceThreshold

int	mic_singleKernel

Bool	useAVXTiles

Detailed Description

Definition at line 100 of file SimParameters.h.

Constructor & Destructor Documentation

SimParameters::SimParameters ( )

inline

Definition at line 1055 of file SimParameters.h.

1055 : mgridforcelist(), parseopts(0) {};

SimParameters::mgridforcelist

MGridforceParamsList mgridforcelist

Definition: SimParameters.h:277

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

inline

Definition at line 1056 of file SimParameters.h.

References initialize_config_data().

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

SimParameters::~SimParameters ( )

inline

Definition at line 1059 of file SimParameters.h.

1059 {};

Member Function Documentation

void SimParameters::close_dcdfile ( )

Definition at line 655 of file Output.C.

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

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

void SimParameters::close_veldcdfile ( )

Definition at line 664 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);
 
 }

BigReal SimParameters::getBondLambda ( const BigReal lambda )

Definition at line 7246 of file SimParameters.C.

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

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

BigReal SimParameters::getCurrentLambda ( const int step )

Definition at line 7167 of file SimParameters.C.

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

                                                       {
   /*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;
   }
 }

BigReal SimParameters::getCurrentLambda2 ( const int step )

Definition at line 7129 of file SimParameters.C.

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

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

BigReal SimParameters::getElecLambda ( const BigReal lambda )

Definition at line 7209 of file SimParameters.C.

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

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

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

Definition at line 104 of file SimParameters.C.

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

BigReal SimParameters::getLambdaDelta ( void )

Definition at line 7203 of file SimParameters.C.

Referenced by Controller::outputTiEnergy().

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

BigReal SimParameters::getRepLambda ( const BigReal lambda )

Definition at line 7241 of file SimParameters.C.

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

BigReal SimParameters::getVdwLambda ( const BigReal lambda )

Definition at line 7223 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);
   }
 }

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

Definition at line 132 of file SimParameters.C.

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

Referenced by SimParameters().

 {
 
    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);
 
 }

int SimParameters::isRecvSpanningTreeOn ( )

inline

Definition at line 1081 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

1081 { return proxyRecvSpanningTree == 1; }

SimParameters::proxyRecvSpanningTree

int proxyRecvSpanningTree

Definition: SimParameters.h:1021

int SimParameters::isRecvSpanningTreeUnset ( )

inline

Definition at line 1082 of file SimParameters.h.

References proxyRecvSpanningTree.

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

1082 { return proxyRecvSpanningTree == -1; }

SimParameters::proxyRecvSpanningTree

int proxyRecvSpanningTree

Definition: SimParameters.h:1021

int SimParameters::isSendSpanningTreeOn ( )

inline

Definition at line 1079 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

1079 { return proxySendSpanningTree == 1; }

SimParameters::proxySendSpanningTree

int proxySendSpanningTree

Definition: SimParameters.h:1020

int SimParameters::isSendSpanningTreeUnset ( )

inline

Definition at line 1080 of file SimParameters.h.

References proxySendSpanningTree.

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

1080 { return proxySendSpanningTree == -1; }

SimParameters::proxySendSpanningTree

int proxySendSpanningTree

Definition: SimParameters.h:1020

int SimParameters::issetinparseopts ( const char * name )

Definition at line 114 of file SimParameters.C.

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

int SimParameters::istrueinparseopts ( const char * name )

Definition at line 109 of file SimParameters.C.

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

void SimParameters::nonbonded_select ( )

static

Definition at line 397 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

                                      {
     ComputeNonbondedUtil::select();
 }

void SimParameters::pme_select ( )

static

Definition at line 401 of file SimParameters.C.

References ComputePmeUtil::select().

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

                                {
   ComputePmeUtil::select();
 }

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

Definition at line 2330 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 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;
        }
        ++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 ( 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);
    }
 
 }

void SimParameters::receive_SimParameters ( MIStream * msg )

Definition at line 7070 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;
 }

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

Definition at line 174 of file SimParameters.C.

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

Referenced by Node::scriptParam().

                                                                   {
 
   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)
   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("outputEnergies",outputEnergies)
   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_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,"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();
     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();
     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();
     return;
   }
 
   if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
     alchLambdaIDWS = atof(value);
     setupIDWS();
     ComputeNonbondedUtil::select();
     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();
     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)) {
     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();
 #ifdef NAMD_CUDA
     // 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();
 #ifdef NAMD_CUDA
     // 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);
 
 }

void SimParameters::send_SimParameters ( MOStream * msg )

Definition at line 7012 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();
 }

int SimParameters::setupIDWS ( )

Definition at line 7139 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.
   */
   alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency;
   if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies;
   if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq;
   if ( alchOutFreq && alchOutFreq != outputEnergies) {
     iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput"
          << " to stdout may not be useful!\n" << endi;
   }
   return 1;
 }

Member Data Documentation

int SimParameters::aaAngleExp

Definition at line 969 of file SimParameters.h.

BigReal SimParameters::accelMDalpha

Definition at line 625 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDDebugOn

Definition at line 620 of file SimParameters.h.

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

Bool SimParameters::accelMDdihe

Definition at line 618 of file SimParameters.h.

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

Bool SimParameters::accelMDdual

Definition at line 619 of file SimParameters.h.

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

BigReal SimParameters::accelMDE

Definition at line 624 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDFirstStep

Definition at line 621 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDG

Definition at line 629 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDPrepSteps

Definition at line 633 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDSteps

Definition at line 631 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiPrepSteps

Definition at line 634 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiSteps

Definition at line 632 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGiE

Definition at line 630 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGresetVaftercmd

Definition at line 640 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGRestart

Definition at line 638 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

char SimParameters::accelMDGRestartFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 639 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDGSigma0D

Definition at line 637 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDGSigma0P

Definition at line 636 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGStatWindow

Definition at line 635 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDLastStep

Definition at line 622 of file SimParameters.h.

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

Bool SimParameters::accelMDOn

Definition at line 617 of file SimParameters.h.

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

int SimParameters::accelMDOutFreq

Definition at line 623 of file SimParameters.h.

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

BigReal SimParameters::accelMDTalpha

Definition at line 627 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::accelMDTE

Definition at line 626 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

BigReal SimParameters::adaptTempAutoDt

Definition at line 651 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempBins

Definition at line 652 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempCgamma

Definition at line 654 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempDebug

Definition at line 644 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

BigReal SimParameters::adaptTempDt

Definition at line 653 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempFirstStep

Definition at line 645 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

int SimParameters::adaptTempFreq

Definition at line 648 of file SimParameters.h.

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

char SimParameters::adaptTempInFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 657 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempLangevin

Definition at line 655 of file SimParameters.h.

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

int SimParameters::adaptTempLastStep

Definition at line 646 of file SimParameters.h.

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

Bool SimParameters::adaptTempOn

Definition at line 643 of file SimParameters.h.

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

int SimParameters::adaptTempOutFreq

Definition at line 647 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRandom

Definition at line 660 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRescale

Definition at line 656 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

char SimParameters::adaptTempRestartFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 658 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempRestartFreq

Definition at line 659 of file SimParameters.h.

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

BigReal SimParameters::adaptTempTmax

Definition at line 650 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempTmin

Definition at line 649 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::alchBondDecouple

Definition at line 436 of file SimParameters.h.

Referenced by CrosstermElem::computeForce().

BigReal SimParameters::alchBondLambdaEnd

Definition at line 430 of file SimParameters.h.

Bool SimParameters::alchDecouple

Definition at line 435 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambdaStart

Definition at line 413 of file SimParameters.h.

Referenced by ComputePmeUtil::select().

Bool SimParameters::alchEnsembleAvg

Definition at line 408 of file SimParameters.h.

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

int SimParameters::alchEquilSteps

Definition at line 410 of file SimParameters.h.

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

Bool SimParameters::alchFepOn

Definition at line 390 of file SimParameters.h.

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

Bool SimParameters::alchFepOnAtStartup

Definition at line 387 of file SimParameters.h.

int SimParameters::alchIDWSFreq

Definition at line 399 of file SimParameters.h.

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

BigReal SimParameters::alchLambda

Definition at line 396 of file SimParameters.h.

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

BigReal SimParameters::alchLambda2

Definition at line 397 of file SimParameters.h.

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

int SimParameters::alchLambdaFreq

Definition at line 400 of file SimParameters.h.

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

BigReal SimParameters::alchLambdaIDWS

Definition at line 398 of file SimParameters.h.

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

int SimParameters::alchMethod

Definition at line 395 of file SimParameters.h.

Bool SimParameters::alchOnAtStartup

Definition at line 386 of file SimParameters.h.

char SimParameters::alchOutFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 409 of file SimParameters.h.

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

int SimParameters::alchOutFreq

Definition at line 407 of file SimParameters.h.

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

BigReal SimParameters::alchRepLambdaEnd

Definition at line 424 of file SimParameters.h.

BigReal SimParameters::alchTemp

Definition at line 406 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOn

Definition at line 393 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOnAtStartup

Definition at line 388 of file SimParameters.h.

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 419 of file SimParameters.h.

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 411 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::alchWCAOn

Definition at line 394 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::alpha_cutoff

Definition at line 530 of file SimParameters.h.

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

BigReal SimParameters::alpha_max

Definition at line 531 of file SimParameters.h.

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

Bool SimParameters::amberOn

Definition at line 990 of file SimParameters.h.

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

char SimParameters::auxFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 211 of file SimParameters.h.

Referenced by CollectionMaster::receiveDataStream().

Bool SimParameters::benchTimestep

Definition at line 167 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureCompressibility

Definition at line 684 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

int SimParameters::berendsenPressureFreq

Definition at line 686 of file SimParameters.h.

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

Bool SimParameters::berendsenPressureOn

Definition at line 682 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 685 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

BigReal SimParameters::berendsenPressureTarget

Definition at line 683 of file SimParameters.h.

Referenced by Controller::berendsenPressure().

Bool SimParameters::binaryOutput

Definition at line 228 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Bool SimParameters::binaryRestart

Definition at line 226 of file SimParameters.h.

char* SimParameters::binAtomFile

Definition at line 1028 of file SimParameters.h.

char* SimParameters::binCoorFile

Definition at line 1029 of file SimParameters.h.

char* SimParameters::binRefFile

Definition at line 1031 of file SimParameters.h.

char* SimParameters::binVelFile

Definition at line 1030 of file SimParameters.h.

int SimParameters::bondedCUDA

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

Definition at line 803 of file SimParameters.h.

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

zVector SimParameters::cellBasisVector1

Definition at line 127 of file SimParameters.h.

zVector SimParameters::cellBasisVector2

Definition at line 128 of file SimParameters.h.

zVector SimParameters::cellBasisVector3

Definition at line 129 of file SimParameters.h.

zVector SimParameters::cellOrigin

Definition at line 130 of file SimParameters.h.

Bool SimParameters::COLDOn

Definition at line 584 of file SimParameters.h.

BigReal SimParameters::COLDRate

Definition at line 586 of file SimParameters.h.

BigReal SimParameters::COLDTemp

Definition at line 587 of file SimParameters.h.

Bool SimParameters::colvarsOn

Definition at line 561 of file SimParameters.h.

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

Bool SimParameters::commOnly

Definition at line 929 of file SimParameters.h.

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

Bool SimParameters::comMove

Definition at line 189 of file SimParameters.h.

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

char SimParameters::computeMapFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 1037 of file SimParameters.h.

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

char SimParameters::consForceFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 881 of file SimParameters.h.

Bool SimParameters::consForceOn

Definition at line 880 of file SimParameters.h.

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

BigReal SimParameters::consForceScaling

Definition at line 882 of file SimParameters.h.

Referenced by ComputeConsForce::doForce().

char SimParameters::consTorqueAxisFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 342 of file SimParameters.h.

char SimParameters::consTorqueFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 340 of file SimParameters.h.

BigReal SimParameters::consTorqueGlobVal

Definition at line 344 of file SimParameters.h.

Referenced by ComputeConsTorque::doForce().

Bool SimParameters::consTorqueOn

Definition at line 339 of file SimParameters.h.

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

char SimParameters::consTorquePivotFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 343 of file SimParameters.h.

char SimParameters::consTorqueValFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 345 of file SimParameters.h.

int SimParameters::constraintExp

Definition at line 263 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

BigReal SimParameters::constraintScaling

Definition at line 291 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

Bool SimParameters::constraintsOn

Definition at line 261 of file SimParameters.h.

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

Bool SimParameters::constrXOn

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::constrYOn

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::constrZOn

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::cosAngles

Definition at line 550 of file SimParameters.h.

Referenced by Parameters::Parameters().

BigReal SimParameters::coulomb_radius_offset

Definition at line 524 of file SimParameters.h.

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

BigReal SimParameters::cutoff

Definition at line 230 of file SimParameters.h.

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

char SimParameters::cylindricalBCAxis

Definition at line 851 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

int SimParameters::cylindricalBCexp1

Definition at line 856 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

int SimParameters::cylindricalBCexp2

Definition at line 857 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCk1

Definition at line 858 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCk2

Definition at line 859 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCl1

Definition at line 854 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCl2

Definition at line 855 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Bool SimParameters::cylindricalBCOn

Definition at line 848 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::cylindricalBCr1

Definition at line 852 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCr2

Definition at line 853 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

zVector SimParameters::cylindricalCenter

Definition at line 850 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::daCutoffDist

Definition at line 976 of file SimParameters.h.

BigReal SimParameters::daOffDist

Definition at line 976 of file SimParameters.h.

BigReal SimParameters::daOnDist

Definition at line 976 of file SimParameters.h.

char SimParameters::dcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 212 of file SimParameters.h.

int SimParameters::dcdFrequency

Definition at line 202 of file SimParameters.h.

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

int SimParameters::dcdUnitCell

Definition at line 204 of file SimParameters.h.

Referenced by Output::coordinate().

BigReal SimParameters::dhaCutoffAngle

Definition at line 972 of file SimParameters.h.

BigReal SimParameters::dhaOffAngle

Definition at line 972 of file SimParameters.h.

BigReal SimParameters::dhaOnAngle

Definition at line 972 of file SimParameters.h.

BigReal SimParameters::dielectric

Definition at line 196 of file SimParameters.h.

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

Bool SimParameters::dihedralOn

Definition at line 583 of file SimParameters.h.

Bool SimParameters::disableTopology

Definition at line 164 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

int SimParameters::distAttExp

Definition at line 969 of file SimParameters.h.

int SimParameters::distRepExp

Definition at line 969 of file SimParameters.h.

BigReal SimParameters::drudeBondConst

Definition at line 542 of file SimParameters.h.

Referenced by BondElem::computeForce().

BigReal SimParameters::drudeBondLen

Definition at line 540 of file SimParameters.h.

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

BigReal SimParameters::drudeDamping

Definition at line 538 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::drudeHardWallOn

Definition at line 536 of file SimParameters.h.

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

BigReal SimParameters::drudeNbtholeCut

Definition at line 543 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::drudeOn

Definition at line 535 of file SimParameters.h.

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

BigReal SimParameters::drudeTemp

Definition at line 537 of file SimParameters.h.

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

BigReal SimParameters::dt

Definition at line 123 of file SimParameters.h.

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

zVector SimParameters::eField

Definition at line 863 of file SimParameters.h.

Referenced by ComputeEField::doForce().

BigReal SimParameters::eFieldFreq

Definition at line 864 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Bool SimParameters::eFieldNormalized

Definition at line 862 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Bool SimParameters::eFieldOn

Definition at line 861 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::eFieldPhase

Definition at line 865 of file SimParameters.h.

Referenced by ComputeEField::doForce().

ExclusionSettings SimParameters::exclude

Definition at line 197 of file SimParameters.h.

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

Bool SimParameters::excludeFromPressure

Definition at line 671 of file SimParameters.h.

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

char SimParameters::extCoordFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 461 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

char SimParameters::extForceFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 462 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

char SimParameters::extForcesCommand[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 460 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Bool SimParameters::extForcesOn

Definition at line 459 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::extraBondsCosAngles

Definition at line 877 of file SimParameters.h.

Bool SimParameters::extraBondsCosAnglesSetByUser

Definition at line 878 of file SimParameters.h.

Bool SimParameters::extraBondsOn

Definition at line 876 of file SimParameters.h.

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

Bool SimParameters::FFTWEstimate

Definition at line 817 of file SimParameters.h.

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

Bool SimParameters::FFTWPatient

Definition at line 818 of file SimParameters.h.

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

Bool SimParameters::FFTWUseWisdom

Definition at line 819 of file SimParameters.h.

char SimParameters::FFTWWisdomFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 820 of file SimParameters.h.

char* SimParameters::FFTWWisdomString

Definition at line 821 of file SimParameters.h.

int SimParameters::firstLdbStep

Definition at line 141 of file SimParameters.h.

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

int SimParameters::firstTimestep

Bool SimParameters::fixCellDims

Definition at line 677 of file SimParameters.h.

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

Bool SimParameters::fixCellDimX

Definition at line 678 of file SimParameters.h.

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

Bool SimParameters::fixCellDimY

Definition at line 679 of file SimParameters.h.

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

Bool SimParameters::fixCellDimZ

Definition at line 680 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsForceOutput

Definition at line 565 of file SimParameters.h.

Referenced by CollectionMgr::submitForces().

Bool SimParameters::fixedAtomsForces

Definition at line 564 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsOn

Definition at line 563 of file SimParameters.h.

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

int SimParameters::FMAFFTBlock

Definition at line 724 of file SimParameters.h.

Bool SimParameters::FMAFFTOn

Definition at line 723 of file SimParameters.h.

int SimParameters::FMALevels

Definition at line 721 of file SimParameters.h.

int SimParameters::FMAMp

Definition at line 722 of file SimParameters.h.

Bool SimParameters::FMAOn

Definition at line 720 of file SimParameters.h.

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

BigReal SimParameters::fmaTheta

Definition at line 137 of file SimParameters.h.

int SimParameters::FMMLevels

Definition at line 768 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Bool SimParameters::FMMOn

Definition at line 767 of file SimParameters.h.

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

BigReal SimParameters::FMMPadding

Definition at line 769 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

char SimParameters::forceDcdFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 214 of file SimParameters.h.

int SimParameters::forceDcdFrequency

Definition at line 207 of file SimParameters.h.

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

Bool SimParameters::freeEnergyOn

Definition at line 559 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::fsMax

Definition at line 521 of file SimParameters.h.

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

Bool SimParameters::fullDirectOn

Definition at line 726 of file SimParameters.h.

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

int SimParameters::fullElectFrequency

Definition at line 135 of file SimParameters.h.

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

BigReal SimParameters::gbis_beta

Definition at line 528 of file SimParameters.h.

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

BigReal SimParameters::gbis_delta

Definition at line 527 of file SimParameters.h.

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

BigReal SimParameters::gbis_gamma

Definition at line 529 of file SimParameters.h.

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

Bool SimParameters::GBISOn

Definition at line 520 of file SimParameters.h.

Bool SimParameters::GBISserOn

Definition at line 522 of file SimParameters.h.

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

Bool SimParameters::genCompressedPsf

Definition at line 1012 of file SimParameters.h.

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

Bool SimParameters::globalForcesOn

Definition at line 551 of file SimParameters.h.

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

Bool SimParameters::globalOn

Definition at line 582 of file SimParameters.h.

char SimParameters::goCoordinates[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 302 of file SimParameters.h.

Bool SimParameters::goForcesOn

Definition at line 300 of file SimParameters.h.

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

Bool SimParameters::goGroPair

Definition at line 299 of file SimParameters.h.

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

GoChoices SimParameters::goMethod

Definition at line 304 of file SimParameters.h.

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

char SimParameters::goParameters[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 301 of file SimParameters.h.

Bool SimParameters::gridforcechecksize

Definition at line 274 of file SimParameters.h.

Bool SimParameters::gridforceContA1

Definition at line 269 of file SimParameters.h.

Bool SimParameters::gridforceContA2

Definition at line 270 of file SimParameters.h.

Bool SimParameters::gridforceContA3

Definition at line 271 of file SimParameters.h.

Bool SimParameters::gridforceLite

Definition at line 273 of file SimParameters.h.

Bool SimParameters::gridforceOn

Definition at line 266 of file SimParameters.h.

zVector SimParameters::gridforceScale

Definition at line 268 of file SimParameters.h.

zVector SimParameters::gridforceVOffset

Definition at line 272 of file SimParameters.h.

Bool SimParameters::gridforceVolts

Definition at line 267 of file SimParameters.h.

Bool SimParameters::gromacsOn

Definition at line 995 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::haAngleExp

Definition at line 969 of file SimParameters.h.

BigReal SimParameters::hgroupCutoff

Definition at line 913 of file SimParameters.h.

Referenced by HomePatch::doGroupSizeCheck().

int SimParameters::hybridGroupSize

Definition at line 145 of file SimParameters.h.

Referenced by NamdHybridLB::NamdHybridLB().

Bool SimParameters::HydrogenBonds

Definition at line 959 of file SimParameters.h.

Bool SimParameters::ignoreMass

Definition at line 910 of file SimParameters.h.

int SimParameters::IMDfreq

Definition at line 981 of file SimParameters.h.

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

int SimParameters::IMDignore

Definition at line 984 of file SimParameters.h.

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

int SimParameters::IMDignoreForces

Definition at line 986 of file SimParameters.h.

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

int SimParameters::IMDon

Definition at line 979 of file SimParameters.h.

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

int SimParameters::IMDport

Definition at line 980 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDwait

Definition at line 982 of file SimParameters.h.

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

BigReal SimParameters::initialTemp

Definition at line 187 of file SimParameters.h.

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

BigReal SimParameters::ion_concentration

Definition at line 526 of file SimParameters.h.

BigReal SimParameters::kappa

Definition at line 525 of file SimParameters.h.

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

Bool SimParameters::langevin_useBAOAB

Definition at line 572 of file SimParameters.h.

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

BigReal SimParameters::langevinDamping

Definition at line 570 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinHydrogen

Definition at line 571 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinOn

Definition at line 568 of file SimParameters.h.

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

Bool SimParameters::langevinOnAtStartup

Definition at line 567 of file SimParameters.h.

Bool SimParameters::langevinPistonBarrier

Definition at line 689 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

BigReal SimParameters::langevinPistonDecay

Definition at line 692 of file SimParameters.h.

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

Bool SimParameters::langevinPistonOn

Definition at line 688 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonPeriod

Definition at line 691 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTarget

Definition at line 690 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTemp

Definition at line 693 of file SimParameters.h.

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

BigReal SimParameters::langevinTemp

Definition at line 569 of file SimParameters.h.

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

int SimParameters::lastLdbStep

Definition at line 143 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

Lattice SimParameters::lattice

Definition at line 131 of file SimParameters.h.

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

Bool SimParameters::LCPOOn

Definition at line 532 of file SimParameters.h.

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

int SimParameters::ldBalancer

Definition at line 138 of file SimParameters.h.

Referenced by LdbCoordinator::createLoadBalancer().

BigReal SimParameters::ldbBackgroundScaling

Definition at line 146 of file SimParameters.h.

BigReal SimParameters::ldbHomeBackgroundScaling

Definition at line 148 of file SimParameters.h.

int SimParameters::ldbPeriod

Definition at line 140 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

BigReal SimParameters::ldbPMEBackgroundScaling

Definition at line 147 of file SimParameters.h.

BigReal SimParameters::ldbRelativeGrainsize

Definition at line 149 of file SimParameters.h.

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

int SimParameters::ldbStrategy

Definition at line 139 of file SimParameters.h.

Referenced by NamdCentLB::Strategy().

Bool SimParameters::ldbUnloadOne

Definition at line 181 of file SimParameters.h.

Bool SimParameters::ldbUnloadOutputPEs

Definition at line 182 of file SimParameters.h.

Bool SimParameters::ldbUnloadPME

Definition at line 179 of file SimParameters.h.

Bool SimParameters::ldbUnloadZero

Definition at line 180 of file SimParameters.h.

int SimParameters::lesFactor

Definition at line 441 of file SimParameters.h.

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

Bool SimParameters::lesOn

Definition at line 440 of file SimParameters.h.

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

Bool SimParameters::lesReduceMass

Definition at line 443 of file SimParameters.h.

Bool SimParameters::lesReduceTemp

Definition at line 442 of file SimParameters.h.

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

BigReal SimParameters::limitDist

Definition at line 237 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::LJcorrection

Definition at line 122 of file SimParameters.h.

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

Bool SimParameters::loadComputeMap

Definition at line 1039 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::lonepairs

Definition at line 119 of file SimParameters.h.

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

int SimParameters::longSplitting

Definition at line 907 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::loweAndersenCutoff

Definition at line 579 of file SimParameters.h.

Bool SimParameters::loweAndersenOn

Definition at line 576 of file SimParameters.h.

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

BigReal SimParameters::loweAndersenRate

Definition at line 578 of file SimParameters.h.

BigReal SimParameters::loweAndersenTemp

Definition at line 577 of file SimParameters.h.

Referenced by colvarproxy_namd::colvarproxy_namd().

Bool SimParameters::mallocTest

Definition at line 1016 of file SimParameters.h.

Referenced by Node::startup().

BigReal SimParameters::margin

Definition at line 231 of file SimParameters.h.

Referenced by HomePatch::doMarginCheck().

Bool SimParameters::martiniDielAllow

Definition at line 247 of file SimParameters.h.

Bool SimParameters::martiniSwitching

Definition at line 245 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

int SimParameters::maxExclusionFlags

Definition at line 947 of file SimParameters.h.

BigReal SimParameters::maximumMove

Definition at line 833 of file SimParameters.h.

Referenced by Sequencer::maximumMove().

int SimParameters::maxPairPart

Definition at line 935 of file SimParameters.h.

int SimParameters::maxPatches

Definition at line 178 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::maxSelfPart

Definition at line 933 of file SimParameters.h.

Bool SimParameters::mergeCrossterms

Definition at line 899 of file SimParameters.h.

Referenced by Controller::printEnergies().

MGridforceParamsList SimParameters::mgridforcelist

Definition at line 277 of file SimParameters.h.

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

Bool SimParameters::mgridforceOn

Definition at line 276 of file SimParameters.h.

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

int SimParameters::mic_deviceThreshold

Definition at line 1047 of file SimParameters.h.

int SimParameters::mic_hostSplit

Definition at line 1042 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p1

Definition at line 1044 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p2

Definition at line 1045 of file SimParameters.h.

int SimParameters::mic_numParts_self_p1

Definition at line 1043 of file SimParameters.h.

int SimParameters::mic_singleKernel

Definition at line 1048 of file SimParameters.h.

int SimParameters::mic_unloadMICPEs

Definition at line 1046 of file SimParameters.h.

int SimParameters::minAtomsPerPatch

Definition at line 945 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

BigReal SimParameters::minBabyStep

Definition at line 830 of file SimParameters.h.

Bool SimParameters::minimizeCGOn

Definition at line 827 of file SimParameters.h.

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

Bool SimParameters::minimizeOn

Definition at line 832 of file SimParameters.h.

Referenced by Sequencer::minimizationQuenchVelocity().

BigReal SimParameters::minLineGoal

Definition at line 831 of file SimParameters.h.

Referenced by Controller::minimize().

BigReal SimParameters::minTinyStep

Definition at line 829 of file SimParameters.h.

Bool SimParameters::minVerbose

Definition at line 828 of file SimParameters.h.

Referenced by Controller::minimize().

Bool SimParameters::miscForcesOn

Definition at line 560 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

int SimParameters::mollyIter

Definition at line 917 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

int SimParameters::mollyOn

Definition at line 915 of file SimParameters.h.

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

BigReal SimParameters::mollyTol

Definition at line 916 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

char SimParameters::movDragFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 322 of file SimParameters.h.

BigReal SimParameters::movDragGlobVel

Definition at line 324 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

Bool SimParameters::movDragOn

Definition at line 321 of file SimParameters.h.

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

char SimParameters::movDragVelFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 325 of file SimParameters.h.

Bool SimParameters::movingConstraintsOn

Definition at line 308 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

zVector SimParameters::movingConsVel

Definition at line 310 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

int SimParameters::MSMApprox

Definition at line 736 of file SimParameters.h.

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

int SimParameters::MSMBlockSizeX

Definition at line 746 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

int SimParameters::MSMBlockSizeY

Definition at line 747 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

int SimParameters::MSMBlockSizeZ

Definition at line 748 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMGridSpacing

Definition at line 750 of file SimParameters.h.

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

int SimParameters::MSMLevels

Definition at line 742 of file SimParameters.h.

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

Bool SimParameters::MSMOn

Definition at line 729 of file SimParameters.h.

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

BigReal SimParameters::MSMPadding

Definition at line 752 of file SimParameters.h.

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

int SimParameters::MSMQuality

Definition at line 732 of file SimParameters.h.

Bool SimParameters::MsmSerialOn

Definition at line 765 of file SimParameters.h.

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

int SimParameters::MSMSplit

Definition at line 739 of file SimParameters.h.

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

BigReal SimParameters::MSMxmax

Definition at line 759 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMxmin

Definition at line 758 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMymax

Definition at line 761 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMymin

Definition at line 760 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMzmax

Definition at line 763 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

BigReal SimParameters::MSMzmin

Definition at line 762 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

MTSChoices SimParameters::MTSAlgorithm

Definition at line 904 of file SimParameters.h.

Referenced by Sequencer::integrate().

int SimParameters::multigratorNoseHooverChainLength

Definition at line 702 of file SimParameters.h.

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

Bool SimParameters::multigratorOn

Definition at line 695 of file SimParameters.h.

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

int SimParameters::multigratorPressureFreq

Definition at line 698 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureRelaxationTime

Definition at line 697 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureTarget

Definition at line 696 of file SimParameters.h.

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

int SimParameters::multigratorTemperatureFreq

Definition at line 701 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureRelaxationTime

Definition at line 700 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureTarget

Definition at line 699 of file SimParameters.h.

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

int SimParameters::N

Definition at line 124 of file SimParameters.h.

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

int SimParameters::nonbondedFrequency

Definition at line 133 of file SimParameters.h.

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

BigReal SimParameters::nonbondedScaling

Definition at line 201 of file SimParameters.h.

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

Bool SimParameters::noPatchesOnOne

Definition at line 185 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnOutputPEs

Definition at line 184 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnZero

Definition at line 183 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::numAtomsPair

Definition at line 941 of file SimParameters.h.

int SimParameters::numAtomsPair2

Definition at line 943 of file SimParameters.h.

int SimParameters::numAtomsSelf

Definition at line 937 of file SimParameters.h.

int SimParameters::numAtomsSelf2

Definition at line 939 of file SimParameters.h.

int SimParameters::numinputprocs

Definition at line 1027 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::numoutputprocs

Definition at line 1034 of file SimParameters.h.

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

int SimParameters::numoutputwrts

Definition at line 1035 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::numTraceSteps

Definition at line 152 of file SimParameters.h.

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

int SimParameters::outputCudaTiming

Definition at line 893 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::finishReductions().

int SimParameters::outputEnergies

Definition at line 884 of file SimParameters.h.

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

char SimParameters::outputFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 216 of file SimParameters.h.

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

Bool SimParameters::outputMaps

Definition at line 160 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

int SimParameters::outputMomenta

Definition at line 887 of file SimParameters.h.

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

int SimParameters::outputPairlists

Definition at line 259 of file SimParameters.h.

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

Bool SimParameters::outputPatchDetails

Definition at line 949 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

int SimParameters::outputPressure

Definition at line 896 of file SimParameters.h.

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

int SimParameters::outputTiming

Definition at line 890 of file SimParameters.h.

Referenced by Controller::printTiming().

int SimParameters::pairInteractionGroup1

Definition at line 546 of file SimParameters.h.

int SimParameters::pairInteractionGroup2

Definition at line 547 of file SimParameters.h.

Bool SimParameters::pairInteractionOn

Definition at line 545 of file SimParameters.h.

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

Bool SimParameters::pairInteractionSelf

Definition at line 548 of file SimParameters.h.

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

BigReal SimParameters::pairlistDist

Definition at line 249 of file SimParameters.h.

BigReal SimParameters::pairlistGrow

Definition at line 257 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

int SimParameters::pairlistMinProcs

Definition at line 251 of file SimParameters.h.

BigReal SimParameters::pairlistShrink

Definition at line 256 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

int SimParameters::pairlistsPerCycle

Definition at line 255 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects().

BigReal SimParameters::pairlistTrigger

Definition at line 258 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Bool SimParameters::paraTypeCharmmOn

Definition at line 295 of file SimParameters.h.

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

Bool SimParameters::paraTypeXplorOn

Definition at line 294 of file SimParameters.h.

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

BigReal SimParameters::patchDimension

Definition at line 232 of file SimParameters.h.

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

Bool SimParameters::PMEBarrier

Definition at line 782 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 773 of file SimParameters.h.

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

int SimParameters::PMEGridSizeX

Definition at line 775 of file SimParameters.h.

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

int SimParameters::PMEGridSizeY

Definition at line 776 of file SimParameters.h.

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

int SimParameters::PMEGridSizeZ

Definition at line 777 of file SimParameters.h.

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

BigReal SimParameters::PMEGridSpacing

Definition at line 778 of file SimParameters.h.

int SimParameters::PMEInterpOrder

Definition at line 774 of file SimParameters.h.

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

int SimParameters::PMEMinPoints

Definition at line 781 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEMinSlices

Definition at line 780 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Bool SimParameters::PMEOffload

Definition at line 790 of file SimParameters.h.

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

Bool SimParameters::PMEOn

Definition at line 771 of file SimParameters.h.

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

int SimParameters::PMEPencils

Definition at line 783 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEPencilsX

Definition at line 784 of file SimParameters.h.

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

int SimParameters::PMEPencilsXLayout

Definition at line 788 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEPencilsY

Definition at line 785 of file SimParameters.h.

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

int SimParameters::PMEPencilsYLayout

Definition at line 787 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMEPencilsZ

Definition at line 786 of file SimParameters.h.

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

int SimParameters::PMEProcessors

Definition at line 779 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

int SimParameters::PMESendOrder

Definition at line 789 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize_pencils().

BigReal SimParameters::PMETolerance

Definition at line 772 of file SimParameters.h.

int SimParameters::pressureProfileAtomTypes

Definition at line 709 of file SimParameters.h.

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

Bool SimParameters::pressureProfileEwaldOn

Definition at line 710 of file SimParameters.h.

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

int SimParameters::pressureProfileEwaldX

Definition at line 711 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldY

Definition at line 712 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldZ

Definition at line 713 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileFreq

Definition at line 708 of file SimParameters.h.

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

Bool SimParameters::pressureProfileOn

Definition at line 706 of file SimParameters.h.

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

int SimParameters::pressureProfileSlabs

Definition at line 707 of file SimParameters.h.

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

Bool SimParameters::printBadContacts

Definition at line 517 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Bool SimParameters::printExclusions

Definition at line 1017 of file SimParameters.h.

int SimParameters::proxyRecvSpanningTree

Definition at line 1021 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

int SimParameters::proxySendSpanningTree

Definition at line 1020 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

int SimParameters::proxyTreeBranchFactor

Definition at line 1023 of file SimParameters.h.

Referenced by Node::startup().

char SimParameters::qmBaseDir[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 475 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmBondColumn[16]

Definition at line 485 of file SimParameters.h.

Bool SimParameters::qmBondDist

Definition at line 486 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmBondOn

Definition at line 484 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmBondScheme

Definition at line 490 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmBondSchemeS[16]

Definition at line 489 of file SimParameters.h.

int SimParameters::qmBondValType

Definition at line 487 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmBondValueTypeS[16]

Definition at line 488 of file SimParameters.h.

Bool SimParameters::qmChrgFromPSF

Definition at line 469 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmChrgMode

Definition at line 473 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmChrgModeS[16]

Definition at line 472 of file SimParameters.h.

char SimParameters::qmColumn[16]

Definition at line 474 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmCSMD

Definition at line 510 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmCSMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 511 of file SimParameters.h.

Bool SimParameters::qmCustomPCSel

Definition at line 502 of file SimParameters.h.

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

Bool SimParameters::qmElecEmbed

Definition at line 500 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmEnergyOutFreq

Definition at line 513 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

char SimParameters::qmExecPath[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 470 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmForcesOn

Definition at line 466 of file SimParameters.h.

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

int SimParameters::qmFormat

Definition at line 480 of file SimParameters.h.

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

int SimParameters::qmLSSFreq

Definition at line 505 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmLSSMode

Definition at line 508 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmLSSModeS[16]

Definition at line 507 of file SimParameters.h.

Bool SimParameters::qmLSSOn

Definition at line 504 of file SimParameters.h.

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

char SimParameters::qmLSSResname[5]

Definition at line 506 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmMOPACAddConfigChrg

Definition at line 482 of file SimParameters.h.

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

Bool SimParameters::qmNoPC

Definition at line 499 of file SimParameters.h.

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

int SimParameters::qmOutFreq

Definition at line 514 of file SimParameters.h.

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

char SimParameters::qmParamPDB[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 467 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::qmParamPDBDefined

Definition at line 468 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::qmPCScheme

Definition at line 495 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSchemeS[16]

Definition at line 494 of file SimParameters.h.

int SimParameters::qmPCSelFreq

Definition at line 501 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmPCSwitchOn

Definition at line 491 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmPCSwitchType

Definition at line 493 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSwitchTypeS[16]

Definition at line 492 of file SimParameters.h.

int SimParameters::qmPosOutFreq

Definition at line 515 of file SimParameters.h.

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

char SimParameters::qmPrepProc[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 478 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmPrepProcOn

Definition at line 479 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmReplaceAll

Definition at line 481 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::qmSecProc[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 476 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmSecProcOn

Definition at line 477 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmSimsPerNode

Definition at line 496 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmSoftware[128]

Definition at line 471 of file SimParameters.h.

Bool SimParameters::qmVDW

Definition at line 498 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

unsigned int SimParameters::randomSeed

Definition at line 718 of file SimParameters.h.

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

Bool SimParameters::readExclusions

Definition at line 991 of file SimParameters.h.

Referenced by buildExclusions().

int SimParameters::reassignFreq

Definition at line 663 of file SimParameters.h.

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

BigReal SimParameters::reassignHold

Definition at line 666 of file SimParameters.h.

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

BigReal SimParameters::reassignIncr

Definition at line 665 of file SimParameters.h.

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

BigReal SimParameters::reassignTemp

Definition at line 664 of file SimParameters.h.

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

Bool SimParameters::replicaUniformPatchGrids

Definition at line 951 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::rescaleFreq

Definition at line 614 of file SimParameters.h.

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

BigReal SimParameters::rescaleTemp

Definition at line 615 of file SimParameters.h.

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

char SimParameters::restartFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 221 of file SimParameters.h.

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

int SimParameters::restartFrequency

Definition at line 222 of file SimParameters.h.

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

Bool SimParameters::restartSave

Definition at line 224 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::restartSaveDcd

Definition at line 225 of file SimParameters.h.

int SimParameters::rigidBonds

Definition at line 919 of file SimParameters.h.

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

int SimParameters::rigidDie

Definition at line 924 of file SimParameters.h.

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

int SimParameters::rigidIter

Definition at line 923 of file SimParameters.h.

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

BigReal SimParameters::rigidTol

Definition at line 922 of file SimParameters.h.

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

zVector SimParameters::rotConsAxis

Definition at line 315 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

zVector SimParameters::rotConsPivot

Definition at line 316 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::rotConstraintsOn

Definition at line 313 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

BigReal SimParameters::rotConsVel

Definition at line 317 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

char SimParameters::rotDragAxisFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 332 of file SimParameters.h.

char SimParameters::rotDragFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 330 of file SimParameters.h.

BigReal SimParameters::rotDragGlobVel

Definition at line 334 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

Bool SimParameters::rotDragOn

Definition at line 329 of file SimParameters.h.

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

char SimParameters::rotDragPivotFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 333 of file SimParameters.h.

char SimParameters::rotDragVelFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 335 of file SimParameters.h.

BigReal SimParameters::scale14

Definition at line 199 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::scriptArg1

Definition at line 1001 of file SimParameters.h.

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

BigReal SimParameters::scriptArg2

Definition at line 1002 of file SimParameters.h.

Referenced by HomePatch::exchangeAtoms().

BigReal SimParameters::scriptArg3

Definition at line 1003 of file SimParameters.h.

BigReal SimParameters::scriptArg4

Definition at line 1004 of file SimParameters.h.

BigReal SimParameters::scriptArg5

Definition at line 1005 of file SimParameters.h.

int SimParameters::scriptIntArg1

Definition at line 1006 of file SimParameters.h.

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

int SimParameters::scriptIntArg2

Definition at line 1007 of file SimParameters.h.

char SimParameters::scriptStringArg1[128]

Definition at line 1008 of file SimParameters.h.

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

char SimParameters::scriptStringArg2[128]

Definition at line 1009 of file SimParameters.h.

Bool SimParameters::sdScaling

Definition at line 392 of file SimParameters.h.

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

Bool SimParameters::selectConstraintsOn

Definition at line 280 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

int SimParameters::simulatedNodeSize

Definition at line 163 of file SimParameters.h.

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

int SimParameters::simulatedPEs

Definition at line 162 of file SimParameters.h.

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

Bool SimParameters::simulateInitialMapping

Definition at line 161 of file SimParameters.h.

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

Bool SimParameters::singleTopology

Definition at line 391 of file SimParameters.h.

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

zVector SimParameters::SMDDir

Definition at line 352 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

char SimParameters::SMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 355 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDk

Definition at line 353 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDk2

Definition at line 354 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Bool SimParameters::SMDOn

Definition at line 350 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

int SimParameters::SMDOutputFreq

Definition at line 356 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDVel

Definition at line 351 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Bool SimParameters::soluteScalingAll

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

Definition at line 456 of file SimParameters.h.

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

BigReal SimParameters::soluteScalingFactor

scaling factor for solute interactions

Definition at line 448 of file SimParameters.h.

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

BigReal SimParameters::soluteScalingFactorCharge

optional independent control over scaling factor for electrostatic interactions of solute

Definition at line 450 of file SimParameters.h.

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

BigReal SimParameters::soluteScalingFactorVdw

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

Definition at line 453 of file SimParameters.h.

Bool SimParameters::soluteScalingOn

REST2 (replica exchange solute tempering) on?

Definition at line 446 of file SimParameters.h.

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

BigReal SimParameters::solvent_dielectric

Definition at line 523 of file SimParameters.h.

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

int SimParameters::sphericalBCexp1

Definition at line 845 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

int SimParameters::sphericalBCexp2

Definition at line 846 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCk1

Definition at line 839 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCk2

Definition at line 841 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Bool SimParameters::sphericalBCOn

Definition at line 836 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::sphericalBCr1

Definition at line 843 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCr2

Definition at line 844 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

zVector SimParameters::sphericalCenter

Definition at line 838 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Bool SimParameters::sphericalConstraintsOn

Definition at line 288 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

zVector SimParameters::sphericalConstrCenter

Definition at line 289 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

int SimParameters::splitPatch

Definition at line 912 of file SimParameters.h.

Bool SimParameters::staticAtomAssignment

Definition at line 950 of file SimParameters.h.

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

Bool SimParameters::statsOn

Definition at line 930 of file SimParameters.h.

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

int SimParameters::stepsPerCycle

Definition at line 125 of file SimParameters.h.

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

zVector SimParameters::stirAxis

Definition at line 873 of file SimParameters.h.

Referenced by ComputeStir::ComputeStir().

char SimParameters::stirFilename[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 868 of file SimParameters.h.

BigReal SimParameters::stirK

Definition at line 872 of file SimParameters.h.

Referenced by ComputeStir::doForce().

Bool SimParameters::stirOn

Definition at line 867 of file SimParameters.h.

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

zVector SimParameters::stirPivot

Definition at line 874 of file SimParameters.h.

Referenced by ComputeStir::ComputeStir().

BigReal SimParameters::stirStartingTheta

Definition at line 870 of file SimParameters.h.

BigReal SimParameters::stirVel

Definition at line 871 of file SimParameters.h.

int SimParameters::stochRescaleFreq

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 606 of file SimParameters.h.

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

Bool SimParameters::stochRescaleHeat

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

Definition at line 609 of file SimParameters.h.

Referenced by Controller::printEnergies().

Bool SimParameters::stochRescaleOn

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

Definition at line 593 of file SimParameters.h.

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

BigReal SimParameters::stochRescalePeriod

Timescale (ps) for stochastic velocity rescaling.

Definition at line 603 of file SimParameters.h.

Referenced by Controller::Controller().

BigReal SimParameters::stochRescaleTemp

Temperature for stochastic velocity rescaling.

Definition at line 600 of file SimParameters.h.

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

Bool SimParameters::storeComputeMap

Definition at line 1038 of file SimParameters.h.

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

zVector SimParameters::strainRate

Definition at line 715 of file SimParameters.h.

Referenced by Controller::Controller().

zVector SimParameters::strainRate2

Definition at line 716 of file SimParameters.h.

Referenced by Controller::Controller().

BigReal SimParameters::surface_tension

Definition at line 533 of file SimParameters.h.

Referenced by ComputeLCPO::ComputeLCPO().

BigReal SimParameters::surfaceTensionTarget

Definition at line 704 of file SimParameters.h.

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

Bool SimParameters::switchingActive

Definition at line 239 of file SimParameters.h.

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

BigReal SimParameters::switchingDist

Definition at line 243 of file SimParameters.h.

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

char SimParameters::symmetryFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 380 of file SimParameters.h.

int SimParameters::symmetryFirstFullStep

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryFirstStep

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

BigReal SimParameters::symmetryk

Definition at line 378 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetrykfile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 379 of file SimParameters.h.

int SimParameters::symmetryLastFullStep

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryLastStep

Definition at line 382 of file SimParameters.h.

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

char SimParameters::symmetryMatrixFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 381 of file SimParameters.h.

Bool SimParameters::symmetryOn

Definition at line 377 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Bool SimParameters::symmetryScaleForces

Definition at line 377 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::tableInterpType[128]

Definition at line 363 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

BigReal SimParameters::tableMaxDist

Definition at line 365 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

int SimParameters::tableNumTypes

Definition at line 361 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Real SimParameters::tableSpacing

Definition at line 364 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Bool SimParameters::tabulatedEnergies

Definition at line 360 of file SimParameters.h.

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

char SimParameters::tabulatedEnergiesFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 362 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

char SimParameters::tclBCArgs[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 558 of file SimParameters.h.

Referenced by ComputeTclBC::doWork().

Bool SimParameters::tclBCOn

Definition at line 556 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

char* SimParameters::tclBCScript

Definition at line 557 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Bool SimParameters::tclForcesOn

Definition at line 552 of file SimParameters.h.

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

Bool SimParameters::tclIsThreaded

Definition at line 554 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Bool SimParameters::tCoupleOn

Definition at line 589 of file SimParameters.h.

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

BigReal SimParameters::tCoupleTemp

Definition at line 591 of file SimParameters.h.

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

Bool SimParameters::testOn

Definition at line 928 of file SimParameters.h.

Bool SimParameters::TMDDiffRMSD

Definition at line 369 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile2[NAMD_FILENAME_BUFFER_SIZE]

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDFinalRMSD

Definition at line 374 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDFirstStep

Definition at line 373 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDInitialRMSD

Definition at line 374 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDk

Definition at line 370 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDLastStep

Definition at line 373 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Bool SimParameters::TMDOn

Definition at line 369 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

int SimParameters::TMDOutputFreq

Definition at line 372 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::totalAtoms

Definition at line 932 of file SimParameters.h.

int SimParameters::traceStartStep

Definition at line 151 of file SimParameters.h.

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

int SimParameters::twoAwayX

Definition at line 175 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayY

Definition at line 176 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayZ

Definition at line 177 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::useAntecedent

Definition at line 962 of file SimParameters.h.

Bool SimParameters::useAVXTiles

Definition at line 1051 of file SimParameters.h.

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

Bool SimParameters::useCompressedPsf

Definition at line 1011 of file SimParameters.h.

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

Bool SimParameters::useConstantArea

Definition at line 674 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

Bool SimParameters::useConstantRatio

Definition at line 675 of file SimParameters.h.

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

Bool SimParameters::useCUDA2

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

Definition at line 798 of file SimParameters.h.

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

Bool SimParameters::useCUDAdisable

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

Definition at line 809 of file SimParameters.h.

Bool SimParameters::useDPME

Definition at line 792 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::useFlexibleCell

Definition at line 673 of file SimParameters.h.

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

Bool SimParameters::useGroupPressure

Definition at line 668 of file SimParameters.h.

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