SimParameters Class Reference

#include <SimParameters.h>

List of all members.

Public Member Functions
	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 *)
int	isSendSpanningTreeOn ()
int	isSendSpanningTreeUnset ()
int	isRecvSpanningTreeOn ()
int	isRecvSpanningTreeUnset ()
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	benchTimestep
int	useNodeHelper
int	twoAwayX
int	twoAwayY
int	twoAwayZ
int	maxPatches
Bool	ldbUnloadPME
Bool	ldbUnloadZero
Bool	ldbUnloadOne
Bool	noPatchesOnZero
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 [128]
char	dcdFilename [128]
char	velDcdFilename [128]
char	forceDcdFilename [128]
char	xstFilename [128]
char	outputFilename [128]
char	restartFilename [128]
int	restartFrequency
Bool	restartSave
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	mgridforceOn
MGridforceParamsList	mgridforcelist
Bool	selectConstraintsOn
Bool	constrXOn
Bool	constrYOn
Bool	constrZOn
BigReal	constraintScaling
Bool	paraTypeXplorOn
Bool	paraTypeCharmmOn
Bool	goForcesOn
char	goParameters [128]
char	goCoordinates [128]
GoChoices	goMethod
Bool	movingConstraintsOn
zVector	movingConsVel
Bool	rotConstraintsOn
zVector	rotConsAxis
zVector	rotConsPivot
BigReal	rotConsVel
Bool	movDragOn
char	movDragFile [128]
BigReal	movDragGlobVel
char	movDragVelFile [128]
Bool	rotDragOn
char	rotDragFile [128]
char	rotDragAxisFile [128]
char	rotDragPivotFile [128]
BigReal	rotDragGlobVel
char	rotDragVelFile [128]
Bool	consTorqueOn
char	consTorqueFile [128]
char	consTorqueAxisFile [128]
char	consTorquePivotFile [128]
BigReal	consTorqueGlobVal
char	consTorqueValFile [128]
Bool	SMDOn
BigReal	SMDVel
zVector	SMDDir
BigReal	SMDk
BigReal	SMDk2
char	SMDFile [128]
int	SMDOutputFreq
Bool	tabulatedEnergies
int	tableNumTypes
char	tabulatedEnergiesFile [128]
char	tableInterpType [128]
Real	tableSpacing
BigReal	tableMaxDist
Bool	TMDOn
Bool	TMDDiffRMSD
BigReal	TMDk
char	TMDFile [128]
char	TMDFile2 [128]
int	TMDOutputFreq
int	TMDFirstStep
int	TMDLastStep
BigReal	TMDInitialRMSD
BigReal	TMDFinalRMSD
Bool	symmetryOn
Bool	symmetryScaleForces
BigReal	symmetryk
char	symmetrykfile [128]
char	symmetryFile [128]
char	symmetryMatrixFile [128]
int	symmetryFirstStep
int	symmetryLastStep
int	symmetryFirstFullStep
int	symmetryLastFullStep
Bool	alchOn
Bool	alchFepOn
Bool	alchThermIntOn
Bool	alchFepWCARepuOn
Bool	alchFepWCADispOn
int	alchMethod
BigReal	alchLambda
BigReal	alchLambda2
BigReal	alchFepWCArcut1
BigReal	alchFepWCArcut2
BigReal	alchTemp
int	alchOutFreq
Bool	alchEnsembleAvg
char	alchOutFile [128]
int	alchEquilSteps
BigReal	alchVdwShiftCoeff
BigReal	alchElecLambdaStart
BigReal	alchVdwLambdaEnd
Bool	alchDecouple
Bool	lesOn
int	lesFactor
Bool	lesReduceTemp
Bool	lesReduceMass
Bool	extForcesOn
char	extForcesCommand [256]
char	extCoordFilename [128]
char	extForceFilename [128]
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
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 [128]
Bool	freeEnergyOn
Bool	miscForcesOn
Bool	colvarsOn
Bool	fixedAtomsOn
Bool	fixedAtomsForces
Bool	langevinOn
BigReal	langevinTemp
BigReal	langevinDamping
Bool	langevinHydrogen
Bool	loweAndersenOn
BigReal	loweAndersenTemp
BigReal	loweAndersenRate
BigReal	loweAndersenCutoff
Bool	globalOn
Bool	dihedralOn
Bool	COLDOn
BigReal	COLDRate
BigReal	COLDTemp
Bool	tCoupleOn
BigReal	tCoupleTemp
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	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 [128]
char	adaptTempRestartFile [128]
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
BigReal	langevinPistonTarget
BigReal	langevinPistonPeriod
BigReal	langevinPistonDecay
BigReal	langevinPistonTemp
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	MSMApprox
int	MSMSplit
int	MSMLevels
int	MSMBlockSizeX
int	MSMBlockSizeY
int	MSMBlockSizeZ
BigReal	MSMGridSpacing
BigReal	MSMPadding
Bool	MsmSerialOn
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
Bool	useDPME
Bool	useOptPME
Bool	useManyToMany
Bool	FFTWEstimate
Bool	FFTWPatient
Bool	FFTWUseWisdom
char	FFTWWisdomFile [128]
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
zVector	eField
BigReal	eFieldFreq
BigReal	eFieldPhase
Bool	stirOn
char	stirFilename [128]
BigReal	stirStartingTheta
BigReal	stirVel
BigReal	stirK
zVector	stirAxis
zVector	stirPivot
Bool	extraBondsOn
Bool	consForceOn
char	consForceFile [128]
BigReal	consForceScaling
int	outputEnergies
int	outputMomenta
int	outputTiming
int	outputCudaTiming
int	outputPressure
Bool	mergeCrossterms
int	firstTimestep
MTSChoices	MTSAlgorithm
int	longSplitting
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	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
Bool	amberOn
Bool	readExclusions
BigReal	vdwscale14
Bool	gromacsOn
Bool	vdwGeometricSigma
BigReal	scriptArg1
BigReal	scriptArg2
BigReal	scriptArg3
BigReal	scriptArg4
BigReal	scriptArg5
Bool	useCompressedPsf
Bool	genCompressedPsf
Bool	usePluginIO
Bool	mallocTest
Bool	printExclusions
int	proxySendSpanningTree
int	proxyRecvSpanningTree
int	proxyTreeBranchFactor
int	numinputprocs
char *	binAtomFile
char *	binCoorFile
char *	binVelFile
int	numoutputprocs
int	numoutputwrts
char	computeMapFilename [128]
Bool	storeComputeMap
Bool	loadComputeMap

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Constructor & Destructor Documentation

SimParameters::SimParameters (   )  [inline]

Definition at line 813 of file SimParameters.h. : mgridforcelist() {};

SimParameters::SimParameters (  ConfigList *  c, char *&  cwd )  [inline]

Definition at line 814 of file SimParameters.h. : mgridforcelist() { initialize_config_data(c,cwd); };

SimParameters::~SimParameters (   )  [inline]

Definition at line 817 of file SimParameters.h. {};

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Member Function Documentation

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

Definition at line 93 of file SimParameters.C. References ParseOptions::check_consistency(), NAMD_die(), and ParseOptions::set(). { ParseOptions opts; // Object to check consistency of config file 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 835 of file SimParameters.h. Referenced by Node::startup(). { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (   )  [inline]

Definition at line 836 of file SimParameters.h. { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (   )  [inline]

Definition at line 833 of file SimParameters.h. Referenced by Node::startup(). { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (   )  [inline]

Definition at line 834 of file SimParameters.h. Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap(). { return proxySendSpanningTree == -1; }

void SimParameters::receive_SimParameters (  MIStream *   )

Definition at line 5770 of file SimParameters.C. References binAtomFile, binCoorFile, binVelFile, MGridforceParamsList::clear(), FFTWWisdomString, MIStream::get(), mgridforcelist, tclBCScript, and MGridforceParamsList::unpack_data(). { 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); } #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 *  , const char *  )

Definition at line 134 of file SimParameters.C. References accelMDalpha, accelMDE, accelMDTalpha, accelMDTE, alchEquilSteps, alchFepWCArcut1, alchFepWCArcut2, alchLambda, alchLambda2, atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, commOnly, consForceScaling, constraintScaling, eField, eFieldFreq, eFieldPhase, firstTimestep, fixCellDims, fixCellDimX, fixCellDimY, fixCellDimZ, fixedAtomsOn, initialTemp, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, N, NAMD_die(), nonbondedScaling, outputFilename, PRESSUREFACTOR, reassignTemp, rescaleTemp, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_MOD_FLOAT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, scriptArg1, scriptArg2, scriptArg3, scriptArg4, scriptArg5, ComputeNonbondedUtil::select(), stirAxis, stirPivot, surfaceTensionTarget, tclBCArgs, useConstantArea, useConstantRatio, useFlexibleCell, and useGroupPressure. 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("numsteps",N) SCRIPT_PARSE_INT("firsttimestep",firstTimestep) SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp) SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp) // SCRIPT_PARSE_BOOL("Langevin",langevinOn) SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp) SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA 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_STRING("outputname",outputFilename) 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_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; } //Modifications for alchemical fep SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps) if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) { alchFepWCArcut1 = atof(value); ComputeNonbondedUtil::select(); return; } if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) { alchFepWCArcut2 = atof(value); ComputeNonbondedUtil::select(); return; } if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) { alchLambda = atof(value); ComputeNonbondedUtil::select(); return; } if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) { alchLambda2 = atof(value); ComputeNonbondedUtil::select(); return; } //fepe // REDUNDANT TI BEGINS // if ( ! strncasecmp(param,"tiLambda",MAX_SCRIPT_PARAM_SIZE) ) { // alchLambda = atof(value); // ComputeNonbondedUtil::select(); // return; // } // REDUNDANT TI ENDS 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; } 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 *   )

Definition at line 5718 of file SimParameters.C. References binAtomFile, binCoorFile, binVelFile, MOStream::end(), FFTWWisdomString, mgridforcelist, MGridforceParamsList::pack_data(), MOStream::put(), and tclBCScript. { /*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); } #endif mgridforcelist.pack_data(msg); msg->end(); }

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Member Data Documentation

int SimParameters::aaAngleExp

Definition at line 746 of file SimParameters.h.

BigReal SimParameters::accelMDalpha

Definition at line 489 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet().

Bool SimParameters::accelMDDebugOn

Definition at line 484 of file SimParameters.h. Referenced by Controller::receivePressure(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().

Bool SimParameters::accelMDdihe

Definition at line 482 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 483 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().

BigReal SimParameters::accelMDE

Definition at line 488 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet().

BigReal SimParameters::accelMDFirstStep

Definition at line 485 of file SimParameters.h. Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().

BigReal SimParameters::accelMDLastStep

Definition at line 486 of file SimParameters.h. Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().

Bool SimParameters::accelMDOn

Definition at line 481 of file SimParameters.h. Referenced by ComputeFullDirect::ComputeFullDirect(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputePme::ComputePme(), Controller::Controller(), OptPmeMgr::initialize(), Sequencer::integrate(), OptPmeCompute::OptPmeCompute(), Controller::receivePressure(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), ComputeGlobal::saveTotalForces(), and ComputeNonbondedUtil::select().

int SimParameters::accelMDOutFreq

Definition at line 487 of file SimParameters.h. Referenced by Controller::receivePressure(), and Controller::rescaleaccelMD().

BigReal SimParameters::accelMDTalpha

Definition at line 491 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet().

BigReal SimParameters::accelMDTE

Definition at line 490 of file SimParameters.h. Referenced by Controller::rescaleaccelMD(), and scriptSet().

BigReal SimParameters::adaptTempAutoDt

Definition at line 502 of file SimParameters.h. Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempBins

Definition at line 503 of file SimParameters.h. Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempCgamma

Definition at line 505 of file SimParameters.h. Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempDebug

Definition at line 495 of file SimParameters.h. Referenced by Controller::adaptTempUpdate().

BigReal SimParameters::adaptTempDt

Definition at line 504 of file SimParameters.h. Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempFirstStep

Definition at line 496 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities().

int SimParameters::adaptTempFreq

Definition at line 499 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), and Controller::adaptTempUpdate().

char SimParameters::adaptTempInFile[128]

Definition at line 508 of file SimParameters.h. Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempLangevin

Definition at line 506 of file SimParameters.h. Referenced by Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2().

int SimParameters::adaptTempLastStep

Definition at line 497 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities().

Bool SimParameters::adaptTempOn

Definition at line 494 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 498 of file SimParameters.h. Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRandom

Definition at line 511 of file SimParameters.h. Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRescale

Definition at line 507 of file SimParameters.h. Referenced by Controller::rescaleVelocities().

char SimParameters::adaptTempRestartFile[128]

Definition at line 509 of file SimParameters.h. Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempRestartFreq

Definition at line 510 of file SimParameters.h. Referenced by Controller::adaptTempInit(), and Controller::adaptTempWriteRestart().

BigReal SimParameters::adaptTempTmax

Definition at line 501 of file SimParameters.h. Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempTmin

Definition at line 500 of file SimParameters.h. Referenced by Controller::adaptTempInit().

Bool SimParameters::alchDecouple

Definition at line 391 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and ComputeNonbondedUtil::select().

BigReal SimParameters::alchElecLambdaStart

Definition at line 382 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), Controller::outputTiEnergy(), and ComputeNonbondedUtil::select().

Bool SimParameters::alchEnsembleAvg

Definition at line 377 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().

int SimParameters::alchEquilSteps

Definition at line 379 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), and scriptSet().

Bool SimParameters::alchFepOn

Definition at line 366 of file SimParameters.h. Referenced by ComputePme::ComputePme(), NamdState::configListInit(), WorkDistrib::createAtomLists(), ComputePmeMgr::initialize(), Controller::outputFepEnergy(), Controller::printFepMessage(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().

Bool SimParameters::alchFepWCADispOn

Definition at line 369 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::alchFepWCArcut1

Definition at line 373 of file SimParameters.h. Referenced by scriptSet(), and ComputeNonbondedUtil::select().

BigReal SimParameters::alchFepWCArcut2

Definition at line 374 of file SimParameters.h. Referenced by scriptSet(), and ComputeNonbondedUtil::select().

Bool SimParameters::alchFepWCARepuOn

Definition at line 368 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::alchLambda

Definition at line 371 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), scriptSet(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces().

BigReal SimParameters::alchLambda2

Definition at line 372 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), scriptSet(), ComputeNonbondedUtil::select(), and ComputePme::ungridForces().

int SimParameters::alchMethod

Definition at line 370 of file SimParameters.h.

Bool SimParameters::alchOn

Definition at line 365 of file SimParameters.h. Referenced by NamdState::configListInit().

char SimParameters::alchOutFile[128]

Definition at line 378 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().

int SimParameters::alchOutFreq

Definition at line 376 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().

BigReal SimParameters::alchTemp

Definition at line 375 of file SimParameters.h. Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), and Controller::writeFepEnergyData().

Bool SimParameters::alchThermIntOn

Definition at line 367 of file SimParameters.h. Referenced by ComputePme::ComputePme(), NamdState::configListInit(), WorkDistrib::createAtomLists(), ComputePmeMgr::initialize(), Controller::outputTiEnergy(), Controller::printTiMessage(), Molecule::receive_Molecule(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 387 of file SimParameters.h. Referenced by Controller::outputTiEnergy(), and ComputeNonbondedUtil::select().

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 380 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::alpha_cutoff

Definition at line 420 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().

BigReal SimParameters::alpha_max

Definition at line 421 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and HomePatch::gbisComputeAfterP1().

Bool SimParameters::amberOn

Definition at line 765 of file SimParameters.h. Referenced by buildExclusions(), and NamdState::configListInit().

char SimParameters::auxFilename[128]

Definition at line 196 of file SimParameters.h. Referenced by CollectionMaster::receiveDataStream().

Bool SimParameters::benchTimestep

Definition at line 154 of file SimParameters.h. Referenced by Output::coordinateNeeded(), Output::forceNeeded(), and Output::velocityNeeded().

BigReal SimParameters::berendsenPressureCompressibility

Definition at line 535 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet().

int SimParameters::berendsenPressureFreq

Definition at line 537 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), and Controller::berendsenPressure().

Bool SimParameters::berendsenPressureOn

Definition at line 533 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), ComputeGridForce::doForce(), OptPmeMgr::initialize(), and scriptSet().

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 536 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet().

BigReal SimParameters::berendsenPressureTarget

Definition at line 534 of file SimParameters.h. Referenced by Controller::berendsenPressure(), and scriptSet().

Bool SimParameters::binaryOutput

Definition at line 212 of file SimParameters.h.

Bool SimParameters::binaryRestart

Definition at line 210 of file SimParameters.h.

char* SimParameters::binAtomFile

Definition at line 799 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binCoorFile

Definition at line 800 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binVelFile

Definition at line 801 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters().

zVector SimParameters::cellBasisVector1

Definition at line 116 of file SimParameters.h.

zVector SimParameters::cellBasisVector2

Definition at line 117 of file SimParameters.h.

zVector SimParameters::cellBasisVector3

Definition at line 118 of file SimParameters.h.

zVector SimParameters::cellOrigin

Definition at line 119 of file SimParameters.h.

Bool SimParameters::COLDOn

Definition at line 469 of file SimParameters.h.

BigReal SimParameters::COLDRate

Definition at line 471 of file SimParameters.h.

BigReal SimParameters::COLDTemp

Definition at line 472 of file SimParameters.h.

Bool SimParameters::colvarsOn

Definition at line 450 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and Sequencer::integrate().

Bool SimParameters::commOnly

Definition at line 707 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), Sequencer::integrate(), scriptSet(), ComputeNonbondedUtil::select(), OptPmeCompute::ungridForces(), and ComputePme::ungridForces().

Bool SimParameters::comMove

Definition at line 174 of file SimParameters.h. Referenced by ParallelIOMgr::bcastMolInfo(), NamdState::configListInit(), WorkDistrib::createAtomLists(), Molecule::num_deg_freedom(), Molecule::num_group_deg_freedom(), Controller::receivePressure(), ParallelIOMgr::recvMolInfo(), and ParallelIOMgr::updateMolInfo().

char SimParameters::computeMapFilename[128]

Definition at line 807 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().

char SimParameters::consForceFile[128]

Definition at line 661 of file SimParameters.h.

Bool SimParameters::consForceOn

Definition at line 660 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

BigReal SimParameters::consForceScaling

Definition at line 662 of file SimParameters.h. Referenced by ComputeConsForce::doForce(), and scriptSet().

char SimParameters::consTorqueAxisFile[128]

Definition at line 319 of file SimParameters.h.

char SimParameters::consTorqueFile[128]

Definition at line 317 of file SimParameters.h.

BigReal SimParameters::consTorqueGlobVal

Definition at line 321 of file SimParameters.h. Referenced by ComputeConsTorque::doForce().

Bool SimParameters::consTorqueOn

Definition at line 316 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::consTorquePivotFile[128]

Definition at line 320 of file SimParameters.h.

char SimParameters::consTorqueValFile[128]

Definition at line 322 of file SimParameters.h.

int SimParameters::constraintExp

Definition at line 247 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

BigReal SimParameters::constraintScaling

Definition at line 269 of file SimParameters.h. Referenced by ComputeRestraints::doForce(), and scriptSet().

Bool SimParameters::constraintsOn

Definition at line 245 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

Bool SimParameters::constrXOn

Definition at line 265 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::constrYOn

Definition at line 265 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::constrZOn

Definition at line 265 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::cosAngles

Definition at line 439 of file SimParameters.h. Referenced by Parameters::Parameters().

BigReal SimParameters::coulomb_radius_offset

Definition at line 414 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeGBISser::doWork(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), ComputeNonbondedCUDA::recvYieldDevice(), and HomePatch::setGBISIntrinsicRadii().

BigReal SimParameters::cutoff

Definition at line 214 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::doMarginCheck(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), OptPmeMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), Sequencer::maximumMove(), Parameters::read_ener_table(), ComputeMsmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

char SimParameters::cylindricalBCAxis

Definition at line 634 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

int SimParameters::cylindricalBCexp1

Definition at line 639 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

int SimParameters::cylindricalBCexp2

Definition at line 640 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCk1

Definition at line 641 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCk2

Definition at line 642 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCl1

Definition at line 637 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCl2

Definition at line 638 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Bool SimParameters::cylindricalBCOn

Definition at line 631 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::cylindricalBCr1

Definition at line 635 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::cylindricalBCr2

Definition at line 636 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

zVector SimParameters::cylindricalCenter

Definition at line 633 of file SimParameters.h. Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

BigReal SimParameters::daCutoffDist

Definition at line 753 of file SimParameters.h.

BigReal SimParameters::daOffDist

Definition at line 753 of file SimParameters.h.

BigReal SimParameters::daOnDist

Definition at line 753 of file SimParameters.h.

char SimParameters::dcdFilename[128]

Definition at line 197 of file SimParameters.h.

int SimParameters::dcdFrequency

Definition at line 187 of file SimParameters.h. Referenced by Output::coordinate(), and Output::coordinateNeeded().

int SimParameters::dcdUnitCell

Definition at line 189 of file SimParameters.h. Referenced by Output::coordinate().

BigReal SimParameters::dhaCutoffAngle

Definition at line 749 of file SimParameters.h.

BigReal SimParameters::dhaOffAngle

Definition at line 749 of file SimParameters.h.

BigReal SimParameters::dhaOnAngle

Definition at line 749 of file SimParameters.h.

BigReal SimParameters::dielectric

Definition at line 181 of file SimParameters.h. Referenced by ComputeMsm::ComputeMsm(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), ComputeMsmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

Bool SimParameters::dihedralOn

Definition at line 468 of file SimParameters.h.

int SimParameters::distAttExp

Definition at line 746 of file SimParameters.h.

int SimParameters::distRepExp

Definition at line 746 of file SimParameters.h.

BigReal SimParameters::drudeBondConst

Definition at line 431 of file SimParameters.h. Referenced by BondElem::computeForce().

BigReal SimParameters::drudeBondLen

Definition at line 429 of file SimParameters.h. Referenced by BondElem::computeForce().

BigReal SimParameters::drudeDamping

Definition at line 427 of file SimParameters.h. Referenced by NamdState::configListInit().

BigReal SimParameters::drudeNbtholeCut

Definition at line 432 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::drudeOn

Definition at line 425 of file SimParameters.h. Referenced by NamdState::configListInit(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), WorkDistrib::mapComputes(), Controller::printEnergies(), Controller::receivePressure(), ComputeNonbondedUtil::select(), and Sequencer::submitReductions().

BigReal SimParameters::drudeTemp

Definition at line 426 of file SimParameters.h. Referenced by Sequencer::langevinVelocitiesBBK2().

BigReal SimParameters::dt

Definition at line 112 of file SimParameters.h. Referenced by Controller::berendsenPressure(), ComputeEField::doForce(), colvarproxy_namd::dt(), Sequencer::integrate(), Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::printEnergies().

zVector SimParameters::eField

Definition at line 645 of file SimParameters.h. Referenced by ComputeEField::doForce(), and scriptSet().

BigReal SimParameters::eFieldFreq

Definition at line 646 of file SimParameters.h. Referenced by ComputeEField::doForce(), and scriptSet().

Bool SimParameters::eFieldOn

Definition at line 644 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::eFieldPhase

Definition at line 647 of file SimParameters.h. Referenced by ComputeEField::doForce(), and scriptSet().

ExclusionSettings SimParameters::exclude

Definition at line 182 of file SimParameters.h. Referenced by buildExclusions(), and ComputeNonbondedUtil::select().

Bool SimParameters::excludeFromPressure

Definition at line 522 of file SimParameters.h. Referenced by NamdState::configListInit(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::extCoordFilename[128]

Definition at line 404 of file SimParameters.h. Referenced by ComputeExtMgr::recvCoord().

char SimParameters::extForceFilename[128]

Definition at line 405 of file SimParameters.h. Referenced by ComputeExtMgr::recvCoord().

char SimParameters::extForcesCommand[256]

Definition at line 403 of file SimParameters.h. Referenced by ComputeExtMgr::recvCoord().

Bool SimParameters::extForcesOn

Definition at line 402 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

Bool SimParameters::extraBondsOn

Definition at line 658 of file SimParameters.h. Referenced by NamdState::configListInit().

Bool SimParameters::FFTWEstimate

Definition at line 600 of file SimParameters.h. Referenced by OptPmeXPencil::fft_init(), OptPmeYPencil::fft_init(), OptPmeZPencil::fft_init(), PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize().

Bool SimParameters::FFTWPatient

Definition at line 601 of file SimParameters.h. Referenced by PmeXPencil::fft_init(), PmeYPencil::fft_init(), PmeZPencil::fft_init(), and ComputePmeMgr::initialize().

Bool SimParameters::FFTWUseWisdom

Definition at line 602 of file SimParameters.h.

char SimParameters::FFTWWisdomFile[128]

Definition at line 603 of file SimParameters.h.

char* SimParameters::FFTWWisdomString

Definition at line 604 of file SimParameters.h. Referenced by receive_SimParameters(), and send_SimParameters().

int SimParameters::firstLdbStep

Definition at line 130 of file SimParameters.h. Referenced by LdbCoordinator::initialize(), and Controller::printEnergies().

int SimParameters::firstTimestep

Definition at line 681 of file SimParameters.h. Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::algorithm(), colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), Output::force(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiming(), Controller::rescaleaccelMD(), scriptSet(), Output::velocity(), and Controller::writeFepEnergyData().

Bool SimParameters::fixCellDims

Definition at line 528 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().

Bool SimParameters::fixCellDimX

Definition at line 529 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().

Bool SimParameters::fixCellDimY

Definition at line 530 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().

Bool SimParameters::fixCellDimZ

Definition at line 531 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().

Bool SimParameters::fixedAtomsForces

Definition at line 453 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::positionsReady(), and ComputeNonbondedUtil::select().

Bool SimParameters::fixedAtomsOn

Definition at line 452 of file SimParameters.h. Referenced by HomePatch::addForceToMomentum(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), HomePatch::addVelocityToPosition(), ParallelIOMgr::bcastHydroBasedCounter(), Sequencer::berendsenPressure(), ParallelIOMgr::calcAtomsInEachPatch(), NamdState::configListInit(), Sequencer::correctMomentum(), Sequencer::langevinPiston(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::minimizeMoveDownhill(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Sequencer::newMinimizeDirection(), Molecule::num_deg_freedom(), Molecule::num_fixed_atoms(), HomePatch::positionsReady(), HomePatch::rattle1(), HomePatch::rattle2(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Controller::receivePressure(), ParallelIOMgr::recvAtomsCntPerPatch(), Sequencer::reinitVelocities(), ComputeGlobal::saveTotalForces(), scriptSet(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), CollectionMgr::submitForces(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().

int SimParameters::FMAFFTBlock

Definition at line 565 of file SimParameters.h.

Bool SimParameters::FMAFFTOn

Definition at line 564 of file SimParameters.h.

int SimParameters::FMALevels

Definition at line 562 of file SimParameters.h.

int SimParameters::FMAMp

Definition at line 563 of file SimParameters.h.

Bool SimParameters::FMAOn

Definition at line 561 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and ComputeNonbondedUtil::select().

BigReal SimParameters::fmaTheta

Definition at line 126 of file SimParameters.h.

char SimParameters::forceDcdFilename[128]

Definition at line 199 of file SimParameters.h.

int SimParameters::forceDcdFrequency

Definition at line 192 of file SimParameters.h. Referenced by Output::force(), Output::forceNeeded(), and Output::velocity().

Bool SimParameters::freeEnergyOn

Definition at line 448 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and ParallelIOMgr::freeMolSpace().

BigReal SimParameters::fsMax

Definition at line 411 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), and ComputeNonbondedCUDA::recvYieldDevice().

Bool SimParameters::fullDirectOn

Definition at line 567 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), and ComputeNonbondedUtil::select().

int SimParameters::fullElectFrequency

Definition at line 124 of file SimParameters.h. Referenced by Controller::compareChecksums(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), OptPmeMgr::recvEvir(), and Sequencer::runComputeObjects().

BigReal SimParameters::gbis_beta

Definition at line 418 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().

BigReal SimParameters::gbis_delta

Definition at line 417 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().

BigReal SimParameters::gbis_gamma

Definition at line 419 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP1(), and HomePatch::gbisComputeAfterP2().

Bool SimParameters::GBISOn

Definition at line 410 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), ComputeNonbondedCUDA::doWork(), ComputeNonbondedCUDA::finishWork(), Sequencer::integrate(), Sequencer::minimize(), ComputeNonbondedCUDA::noWork(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedCUDA::registerPatches().

Bool SimParameters::GBISserOn

Definition at line 412 of file SimParameters.h. Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes().

Bool SimParameters::genCompressedPsf

Definition at line 783 of file SimParameters.h. Referenced by NamdState::configListInit().

Bool SimParameters::globalForcesOn

Definition at line 440 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and WorkDistrib::mapComputes().

Bool SimParameters::globalOn

Definition at line 467 of file SimParameters.h.

char SimParameters::goCoordinates[128]

Definition at line 279 of file SimParameters.h.

Bool SimParameters::goForcesOn

Definition at line 277 of file SimParameters.h. Referenced by NamdState::configListInit(), Controller::printEnergies(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule().

GoChoices SimParameters::goMethod

Definition at line 281 of file SimParameters.h. Referenced by NamdState::configListInit(), Molecule::receive_GoMolecule(), ComputeNonbondedUtil::select(), and Molecule::send_GoMolecule().

char SimParameters::goParameters[128]

Definition at line 278 of file SimParameters.h.

Bool SimParameters::gridforceContA1

Definition at line 253 of file SimParameters.h.

Bool SimParameters::gridforceContA2

Definition at line 254 of file SimParameters.h.

Bool SimParameters::gridforceContA3

Definition at line 255 of file SimParameters.h.

Bool SimParameters::gridforceLite

Definition at line 257 of file SimParameters.h.

Bool SimParameters::gridforceOn

Definition at line 250 of file SimParameters.h.

zVector SimParameters::gridforceScale

Definition at line 252 of file SimParameters.h.

zVector SimParameters::gridforceVOffset

Definition at line 256 of file SimParameters.h.

Bool SimParameters::gridforceVolts

Definition at line 251 of file SimParameters.h.

Bool SimParameters::gromacsOn

Definition at line 770 of file SimParameters.h. Referenced by NamdState::configListInit().

int SimParameters::haAngleExp

Definition at line 746 of file SimParameters.h.

BigReal SimParameters::hgroupCutoff

Definition at line 691 of file SimParameters.h. Referenced by HomePatch::doGroupSizeCheck().

int SimParameters::hybridGroupSize

Definition at line 134 of file SimParameters.h. Referenced by NamdHybridLB::NamdHybridLB().

Bool SimParameters::HydrogenBonds

Definition at line 736 of file SimParameters.h.

int SimParameters::IMDfreq

Definition at line 758 of file SimParameters.h. Referenced by Output::coordinate(), Output::coordinateNeeded(), and Controller::printEnergies().

int SimParameters::IMDignore

Definition at line 761 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDon

Definition at line 756 of file SimParameters.h. Referenced by Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), and Controller::printEnergies().

int SimParameters::IMDport

Definition at line 757 of file SimParameters.h. Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDwait

Definition at line 759 of file SimParameters.h. Referenced by GlobalMasterIMD::get_vmd_forces(), and GlobalMasterIMD::GlobalMasterIMD().

BigReal SimParameters::initialTemp

Definition at line 172 of file SimParameters.h. Referenced by Controller::adaptTempInit(), Controller::algorithm(), WorkDistrib::createAtomLists(), Sequencer::integrate(), Sequencer::reinitVelocities(), and scriptSet().

BigReal SimParameters::ion_concentration

Definition at line 416 of file SimParameters.h.

BigReal SimParameters::kappa

Definition at line 415 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().

BigReal SimParameters::langevinDamping

Definition at line 457 of file SimParameters.h. Referenced by NamdState::configListInit().

Bool SimParameters::langevinHydrogen

Definition at line 458 of file SimParameters.h. Referenced by NamdState::configListInit().

Bool SimParameters::langevinOn

Definition at line 455 of file SimParameters.h. Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), NamdState::configListInit(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), Molecule::num_deg_freedom(), Molecule::num_group_deg_freedom(), Molecule::receive_Molecule(), Controller::receivePressure(), and Molecule::send_Molecule().

BigReal SimParameters::langevinPistonDecay

Definition at line 542 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().

Bool SimParameters::langevinPistonOn

Definition at line 539 of file SimParameters.h. Referenced by ComputeGridForce::doForce(), OptPmeMgr::initialize(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), scriptSet(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().

BigReal SimParameters::langevinPistonPeriod

Definition at line 541 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().

BigReal SimParameters::langevinPistonTarget

Definition at line 540 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().

BigReal SimParameters::langevinPistonTemp

Definition at line 543 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().

BigReal SimParameters::langevinTemp

Definition at line 456 of file SimParameters.h. Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and scriptSet().

int SimParameters::lastLdbStep

Definition at line 132 of file SimParameters.h. Referenced by LdbCoordinator::initialize().

Lattice SimParameters::lattice

Definition at line 120 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), ParallelIOMgr::calcAtomsInEachPatch(), colvarproxy_namd::colvarproxy_namd(), NamdState::configListInit(), WorkDistrib::createAtomLists(), OptPmeXPencil::fft_init(), GridforceFullMainGrid::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), OptPmeMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), Patch::Patch(), WorkDistrib::patchMapInit(), PatchMgr::setLattice(), and Node::startup().

Bool SimParameters::LCPOOn

Definition at line 422 of file SimParameters.h. Referenced by Sequencer::integrate(), WorkDistrib::mapComputes(), Sequencer::minimize(), Molecule::Molecule(), WorkDistrib::patchMapInit(), Molecule::receive_Molecule(), Molecule::send_Molecule(), and NamdCentLB::Strategy().

int SimParameters::ldBalancer

Definition at line 127 of file SimParameters.h. Referenced by LdbCoordinator::createLoadBalancer(), LdbCoordinator::initialize(), and LdbCoordinator::rebalance().

BigReal SimParameters::ldbBackgroundScaling

Definition at line 135 of file SimParameters.h.

BigReal SimParameters::ldbHomeBackgroundScaling

Definition at line 137 of file SimParameters.h.

int SimParameters::ldbPeriod

Definition at line 129 of file SimParameters.h. Referenced by LdbCoordinator::initialize().

BigReal SimParameters::ldbPMEBackgroundScaling

Definition at line 136 of file SimParameters.h.

BigReal SimParameters::ldbRelativeGrainsize

Definition at line 138 of file SimParameters.h. Referenced by NamdCentLB::Strategy().

int SimParameters::ldbStrategy

Definition at line 128 of file SimParameters.h. Referenced by LdbCoordinator::initialize(), and NamdCentLB::Strategy().

Bool SimParameters::ldbUnloadOne

Definition at line 168 of file SimParameters.h.

Bool SimParameters::ldbUnloadPME

Definition at line 166 of file SimParameters.h.

Bool SimParameters::ldbUnloadZero

Definition at line 167 of file SimParameters.h.

int SimParameters::lesFactor

Definition at line 398 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), Sequencer::reinitVelocities(), and ComputeNonbondedUtil::select().

Bool SimParameters::lesOn

Definition at line 397 of file SimParameters.h. Referenced by ComputePme::ComputePme(), NamdState::configListInit(), WorkDistrib::createAtomLists(), ComputePmeMgr::initialize(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Sequencer::reinitVelocities(), ComputeNonbondedUtil::select(), and Molecule::send_Molecule().

Bool SimParameters::lesReduceMass

Definition at line 400 of file SimParameters.h.

Bool SimParameters::lesReduceTemp

Definition at line 399 of file SimParameters.h. Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().

BigReal SimParameters::limitDist

Definition at line 221 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::LJcorrection

Definition at line 111 of file SimParameters.h. Referenced by Controller::printEnergies(), and Controller::receivePressure().

Bool SimParameters::loadComputeMap

Definition at line 809 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

Bool SimParameters::lonepairs

Definition at line 108 of file SimParameters.h. Referenced by Sequencer::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects().

int SimParameters::longSplitting

Definition at line 687 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::loweAndersenCutoff

Definition at line 464 of file SimParameters.h.

Bool SimParameters::loweAndersenOn

Definition at line 461 of file SimParameters.h. Referenced by Sequencer::integrate().

BigReal SimParameters::loweAndersenRate

Definition at line 463 of file SimParameters.h.

BigReal SimParameters::loweAndersenTemp

Definition at line 462 of file SimParameters.h. Referenced by scriptSet().

Bool SimParameters::mallocTest

Definition at line 787 of file SimParameters.h. Referenced by Node::startup().

BigReal SimParameters::margin

Definition at line 215 of file SimParameters.h. Referenced by HomePatch::doMarginCheck().

Bool SimParameters::martiniDielAllow

Definition at line 231 of file SimParameters.h.

Bool SimParameters::martiniSwitching

Definition at line 229 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

int SimParameters::maxExclusionFlags

Definition at line 725 of file SimParameters.h.

BigReal SimParameters::maximumMove

Definition at line 616 of file SimParameters.h. Referenced by Sequencer::maximumMove().

int SimParameters::maxPairPart

Definition at line 713 of file SimParameters.h.

int SimParameters::maxPatches

Definition at line 165 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

int SimParameters::maxSelfPart

Definition at line 711 of file SimParameters.h.

Bool SimParameters::mergeCrossterms

Definition at line 679 of file SimParameters.h. Referenced by Controller::printEnergies().

MGridforceParamsList SimParameters::mgridforcelist

Definition at line 260 of file SimParameters.h. Referenced by Molecule::build_gridforce_params(), receive_SimParameters(), Node::reloadGridforceGrid(), and send_SimParameters().

Bool SimParameters::mgridforceOn

Definition at line 259 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

int SimParameters::minAtomsPerPatch

Definition at line 723 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

BigReal SimParameters::minBabyStep

Definition at line 613 of file SimParameters.h. Referenced by Controller::minimize().

Bool SimParameters::minimizeCGOn

Definition at line 610 of file SimParameters.h. Referenced by NamdState::configListInit(), and ScriptTcl::run().

Bool SimParameters::minimizeOn

Definition at line 615 of file SimParameters.h. Referenced by Sequencer::minimizationQuenchVelocity().

BigReal SimParameters::minLineGoal

Definition at line 614 of file SimParameters.h. Referenced by Controller::minimize().

BigReal SimParameters::minTinyStep

Definition at line 612 of file SimParameters.h. Referenced by Controller::minimize().

Bool SimParameters::minVerbose

Definition at line 611 of file SimParameters.h. Referenced by Controller::minimize().

Bool SimParameters::miscForcesOn

Definition at line 449 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

int SimParameters::mollyIter

Definition at line 695 of file SimParameters.h. Referenced by HomePatch::mollyAverage().

int SimParameters::mollyOn

Definition at line 693 of file SimParameters.h. Referenced by Controller::compareChecksums(), Sequencer::integrate(), and Sequencer::minimize().

BigReal SimParameters::mollyTol

Definition at line 694 of file SimParameters.h. Referenced by HomePatch::mollyAverage().

char SimParameters::movDragFile[128]

Definition at line 299 of file SimParameters.h.

BigReal SimParameters::movDragGlobVel

Definition at line 301 of file SimParameters.h. Referenced by Sequencer::addMovDragToPosition().

Bool SimParameters::movDragOn

Definition at line 298 of file SimParameters.h. Referenced by NamdState::configListInit(), Sequencer::integrate(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::movDragVelFile[128]

Definition at line 302 of file SimParameters.h.

Bool SimParameters::movingConstraintsOn

Definition at line 285 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

zVector SimParameters::movingConsVel

Definition at line 287 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

int SimParameters::MSMApprox

Definition at line 571 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

int SimParameters::MSMBlockSizeX

Definition at line 574 of file SimParameters.h.

int SimParameters::MSMBlockSizeY

Definition at line 575 of file SimParameters.h.

int SimParameters::MSMBlockSizeZ

Definition at line 576 of file SimParameters.h.

BigReal SimParameters::MSMGridSpacing

Definition at line 577 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

int SimParameters::MSMLevels

Definition at line 573 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

Bool SimParameters::MSMOn

Definition at line 570 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), ComputeNonbondedUtil::select(), and Node::startup().

BigReal SimParameters::MSMPadding

Definition at line 578 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), and ComputeMsmSerialMgr::recvCoord().

Bool SimParameters::MsmSerialOn

Definition at line 579 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and Node::startup().

int SimParameters::MSMSplit

Definition at line 572 of file SimParameters.h. Referenced by ComputeMsmMgr::initialize(), ComputeMsmSerialMgr::recvCoord(), and ComputeNonbondedUtil::select().

MTSChoices SimParameters::MTSAlgorithm

Definition at line 684 of file SimParameters.h. Referenced by Sequencer::integrate().

int SimParameters::N

Definition at line 113 of file SimParameters.h. Referenced by colvarproxy_namd::calculate(), Output::coordinate(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::printEnergies(), Controller::printTiming(), scriptSet(), and Output::velocity().

int SimParameters::nonbondedFrequency

Definition at line 122 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate().

BigReal SimParameters::nonbondedScaling

Definition at line 186 of file SimParameters.h. Referenced by ComputeNonbondedCUDA::recvYieldDevice(), scriptSet(), and ComputeNonbondedUtil::select().

Bool SimParameters::noPatchesOnOne

Definition at line 170 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnZero

Definition at line 169 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

int SimParameters::numAtomsPair

Definition at line 719 of file SimParameters.h.

int SimParameters::numAtomsPair2

Definition at line 721 of file SimParameters.h.

int SimParameters::numAtomsSelf

Definition at line 715 of file SimParameters.h.

int SimParameters::numAtomsSelf2

Definition at line 717 of file SimParameters.h.

int SimParameters::numinputprocs

Definition at line 798 of file SimParameters.h. Referenced by NamdState::configListInit(), and ParallelIOMgr::initialize().

int SimParameters::numoutputprocs

Definition at line 804 of file SimParameters.h. Referenced by NamdState::configListInit(), ParallelIOMgr::initialize(), CollectionMaster::startNextRoundOutputForce(), CollectionMaster::startNextRoundOutputPos(), CollectionMaster::startNextRoundOutputVel(), and CollectionMaster::wrapCoorFinished().

int SimParameters::numoutputwrts

Definition at line 805 of file SimParameters.h. Referenced by NamdState::configListInit(), ParallelIOMgr::initialize(), CollectionMaster::startNextRoundOutputForce(), CollectionMaster::startNextRoundOutputPos(), and CollectionMaster::startNextRoundOutputVel().

int SimParameters::numTraceSteps

Definition at line 141 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate().

int SimParameters::outputCudaTiming

Definition at line 673 of file SimParameters.h. Referenced by ComputeNonbondedCUDA::doWork(), and ComputeNonbondedCUDA::finishWork().

int SimParameters::outputEnergies

Definition at line 664 of file SimParameters.h. Referenced by Sequencer::integrate(), Controller::printEnergies(), and Controller::printTiming().

char SimParameters::outputFilename[128]

Definition at line 201 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::outputExtendedSystem(), and scriptSet().

Bool SimParameters::outputMaps

Definition at line 149 of file SimParameters.h. Referenced by Node::outputPatchComputeMaps().

int SimParameters::outputMomenta

Definition at line 667 of file SimParameters.h. Referenced by Controller::printEnergies().

int SimParameters::outputPairlists

Definition at line 243 of file SimParameters.h. Referenced by Controller::compareChecksums(), and Controller::printEnergies().

Bool SimParameters::outputPatchDetails

Definition at line 727 of file SimParameters.h. Referenced by WorkDistrib::createAtomLists().

int SimParameters::outputPressure

Definition at line 676 of file SimParameters.h. Referenced by Controller::printEnergies().

int SimParameters::outputTiming

Definition at line 670 of file SimParameters.h. Referenced by Controller::printTiming().

int SimParameters::pairInteractionGroup1

Definition at line 435 of file SimParameters.h.

int SimParameters::pairInteractionGroup2

Definition at line 436 of file SimParameters.h.

Bool SimParameters::pairInteractionOn

Definition at line 434 of file SimParameters.h. Referenced by ComputePme::ComputePme(), NamdState::configListInit(), WorkDistrib::createAtomLists(), ComputePmeMgr::initialize(), WorkDistrib::mapComputes(), Molecule::num_deg_freedom(), Controller::printEnergies(), Molecule::receive_Molecule(), Controller::receivePressure(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

Bool SimParameters::pairInteractionSelf

Definition at line 437 of file SimParameters.h. Referenced by ComputePme::ComputePme(), NamdState::configListInit(), ComputePmeMgr::initialize(), WorkDistrib::mapComputes(), ComputeNonbondedUtil::select(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

BigReal SimParameters::pairlistDist

Definition at line 233 of file SimParameters.h.

BigReal SimParameters::pairlistGrow

Definition at line 241 of file SimParameters.h. Referenced by HomePatch::doPairlistCheck().

int SimParameters::pairlistMinProcs

Definition at line 235 of file SimParameters.h.

BigReal SimParameters::pairlistShrink

Definition at line 240 of file SimParameters.h. Referenced by HomePatch::doPairlistCheck().

int SimParameters::pairlistsPerCycle

Definition at line 239 of file SimParameters.h. Referenced by Sequencer::runComputeObjects().

BigReal SimParameters::pairlistTrigger

Definition at line 242 of file SimParameters.h. Referenced by HomePatch::doPairlistCheck().

Bool SimParameters::paraTypeCharmmOn

Definition at line 273 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), and Parameters::Parameters().

Bool SimParameters::paraTypeXplorOn

Definition at line 272 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), and Parameters::Parameters().

BigReal SimParameters::patchDimension

Definition at line 216 of file SimParameters.h. Referenced by HomePatch::doMarginCheck(), ComputePmeMgr::initialize(), OptPmeMgr::initialize_pencils(), ComputePmeMgr::initialize_pencils(), and WorkDistrib::patchMapInit().

Bool SimParameters::PMEBarrier

Definition at line 592 of file SimParameters.h. Referenced by ComputePmeMgr::initialize().

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 583 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

int SimParameters::PMEGridSizeX

Definition at line 585 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid().

int SimParameters::PMEGridSizeY

Definition at line 586 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid().

int SimParameters::PMEGridSizeZ

Definition at line 587 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid().

BigReal SimParameters::PMEGridSpacing

Definition at line 588 of file SimParameters.h.

int SimParameters::PMEInterpOrder

Definition at line 584 of file SimParameters.h. Referenced by ComputePme::ComputePme(), ComputePmeMgr::initialize(), and initializePmeGrid().

int SimParameters::PMEMinPoints

Definition at line 591 of file SimParameters.h. Referenced by ComputePmeMgr::initialize(), and initializePmeGrid().

int SimParameters::PMEMinSlices

Definition at line 590 of file SimParameters.h. Referenced by ComputePmeMgr::initialize().

Bool SimParameters::PMEOn

Definition at line 581 of file SimParameters.h. Referenced by WorkDistrib::assignNodeToPatch(), ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), ComputeNonbondedUtil::select(), and Node::startup().

int SimParameters::PMEPencils

Definition at line 593 of file SimParameters.h. Referenced by OptPmeMgr::initialize(), ComputePmeMgr::initialize(), and initializePmeGrid().

int SimParameters::PMEProcessors

Definition at line 589 of file SimParameters.h. Referenced by ComputePmeMgr::initialize().

BigReal SimParameters::PMETolerance

Definition at line 582 of file SimParameters.h.

int SimParameters::pressureProfileAtomTypes

Definition at line 550 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), NamdState::configListInit(), Controller::Controller(), WorkDistrib::createAtomLists(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().

Bool SimParameters::pressureProfileEwaldOn

Definition at line 551 of file SimParameters.h. Referenced by Controller::Controller(), and WorkDistrib::mapComputes().

int SimParameters::pressureProfileEwaldX

Definition at line 552 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldY

Definition at line 553 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldZ

Definition at line 554 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileFreq

Definition at line 549 of file SimParameters.h. Referenced by Controller::Controller(), and Controller::printEnergies().

Bool SimParameters::pressureProfileOn

Definition at line 547 of file SimParameters.h. Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), Controller::Controller(), ComputeNonbondedUtil::select(), and Sequencer::Sequencer().

int SimParameters::pressureProfileSlabs

Definition at line 548 of file SimParameters.h. Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), HomePatch::rattle1(), ComputeNonbondedUtil::select(), Sequencer::Sequencer(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

Bool SimParameters::printBadContacts

Definition at line 407 of file SimParameters.h. Referenced by Sequencer::submitMinimizeReductions().

Bool SimParameters::printExclusions

Definition at line 788 of file SimParameters.h.

int SimParameters::proxyRecvSpanningTree

Definition at line 792 of file SimParameters.h.

int SimParameters::proxySendSpanningTree

Definition at line 791 of file SimParameters.h.

int SimParameters::proxyTreeBranchFactor

Definition at line 794 of file SimParameters.h. Referenced by Node::startup().

unsigned int SimParameters::randomSeed

Definition at line 559 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::Sequencer(), and Node::startup().

Bool SimParameters::readExclusions

Definition at line 766 of file SimParameters.h. Referenced by buildExclusions().

int SimParameters::reassignFreq

Definition at line 514 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::reassignVelocities(), and Controller::reassignVelocities().

BigReal SimParameters::reassignHold

Definition at line 517 of file SimParameters.h. Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().

BigReal SimParameters::reassignIncr

Definition at line 516 of file SimParameters.h. Referenced by Sequencer::reassignVelocities(), and Controller::reassignVelocities().

BigReal SimParameters::reassignTemp

Definition at line 515 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Sequencer::reassignVelocities(), Controller::reassignVelocities(), and scriptSet().

int SimParameters::rescaleFreq

Definition at line 478 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 479 of file SimParameters.h. Referenced by Controller::adaptTempInit(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Controller::rescaleVelocities(), and scriptSet().

char SimParameters::restartFilename[128]

Definition at line 206 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::outputExtendedSystem().

int SimParameters::restartFrequency

Definition at line 207 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), Output::coordinate(), Output::coordinateNeeded(), Controller::outputExtendedSystem(), Output::velocity(), and Output::velocityNeeded().

Bool SimParameters::restartSave

Definition at line 209 of file SimParameters.h. Referenced by Controller::outputExtendedSystem().

int SimParameters::rigidBonds

Definition at line 697 of file SimParameters.h. Referenced by ParallelIOMgr::bcastHydroBasedCounter(), NamdState::configListInit(), WorkDistrib::createAtomLists(), outputCompressedFile(), Sequencer::rattle1(), and Sequencer::rattle2().

int SimParameters::rigidDie

Definition at line 702 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2().

int SimParameters::rigidIter

Definition at line 701 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2().

BigReal SimParameters::rigidTol

Definition at line 700 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2().

zVector SimParameters::rotConsAxis

Definition at line 292 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

zVector SimParameters::rotConsPivot

Definition at line 293 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

Bool SimParameters::rotConstraintsOn

Definition at line 290 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

BigReal SimParameters::rotConsVel

Definition at line 294 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

char SimParameters::rotDragAxisFile[128]

Definition at line 309 of file SimParameters.h.

char SimParameters::rotDragFile[128]

Definition at line 307 of file SimParameters.h.

BigReal SimParameters::rotDragGlobVel

Definition at line 311 of file SimParameters.h. Referenced by Sequencer::addRotDragToPosition().

Bool SimParameters::rotDragOn

Definition at line 306 of file SimParameters.h. Referenced by NamdState::configListInit(), Sequencer::integrate(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

char SimParameters::rotDragPivotFile[128]

Definition at line 310 of file SimParameters.h.

char SimParameters::rotDragVelFile[128]

Definition at line 312 of file SimParameters.h.

BigReal SimParameters::scale14

Definition at line 184 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

BigReal SimParameters::scriptArg1

Definition at line 776 of file SimParameters.h. Referenced by Sequencer::algorithm(), Controller::algorithm(), and scriptSet().

BigReal SimParameters::scriptArg2

Definition at line 777 of file SimParameters.h. Referenced by scriptSet().

BigReal SimParameters::scriptArg3

Definition at line 778 of file SimParameters.h. Referenced by scriptSet().

BigReal SimParameters::scriptArg4

Definition at line 779 of file SimParameters.h. Referenced by scriptSet().

BigReal SimParameters::scriptArg5

Definition at line 780 of file SimParameters.h. Referenced by scriptSet().

Bool SimParameters::selectConstraintsOn

Definition at line 263 of file SimParameters.h. Referenced by ComputeRestraints::ComputeRestraints().

int SimParameters::simulatedNodeSize

Definition at line 152 of file SimParameters.h. Referenced by Node::outputPatchComputeMaps(), and Node::startup().

int SimParameters::simulatedPEs

Definition at line 151 of file SimParameters.h. Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().

Bool SimParameters::simulateInitialMapping

Definition at line 150 of file SimParameters.h. Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().

zVector SimParameters::SMDDir

Definition at line 329 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

char SimParameters::SMDFile[128]

Definition at line 332 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDk

Definition at line 330 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDk2

Definition at line 331 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

Bool SimParameters::SMDOn

Definition at line 327 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

int SimParameters::SMDOutputFreq

Definition at line 333 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

BigReal SimParameters::SMDVel

Definition at line 328 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

BigReal SimParameters::solvent_dielectric

Definition at line 413 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), HomePatch::gbisComputeAfterP2(), and ComputeNonbondedCUDA::recvYieldDevice().

int SimParameters::sphericalBCexp1

Definition at line 628 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

int SimParameters::sphericalBCexp2

Definition at line 629 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCk1

Definition at line 622 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCk2

Definition at line 624 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

Bool SimParameters::sphericalBCOn

Definition at line 619 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::sphericalBCr1

Definition at line 626 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

BigReal SimParameters::sphericalBCr2

Definition at line 627 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

zVector SimParameters::sphericalCenter

Definition at line 621 of file SimParameters.h. Referenced by ComputeSphericalBC::ComputeSphericalBC().

int SimParameters::splitPatch

Definition at line 690 of file SimParameters.h.

Bool SimParameters::staticAtomAssignment

Definition at line 728 of file SimParameters.h. Referenced by WorkDistrib::createAtomLists(), WorkDistrib::patchMapInit(), and HomePatch::positionsReady().

Bool SimParameters::statsOn

Definition at line 708 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate().

int SimParameters::stepsPerCycle

Definition at line 114 of file SimParameters.h. Referenced by LdbCoordinator::initialize(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects().

zVector SimParameters::stirAxis

Definition at line 655 of file SimParameters.h. Referenced by ComputeStir::ComputeStir(), and scriptSet().

char SimParameters::stirFilename[128]

Definition at line 650 of file SimParameters.h.

BigReal SimParameters::stirK

Definition at line 654 of file SimParameters.h. Referenced by ComputeStir::doForce().

Bool SimParameters::stirOn

Definition at line 649 of file SimParameters.h. Referenced by NamdState::configListInit(), WorkDistrib::mapComputes(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

zVector SimParameters::stirPivot

Definition at line 656 of file SimParameters.h. Referenced by ComputeStir::ComputeStir(), and scriptSet().

BigReal SimParameters::stirStartingTheta

Definition at line 652 of file SimParameters.h.

BigReal SimParameters::stirVel

Definition at line 653 of file SimParameters.h.

Bool SimParameters::storeComputeMap

Definition at line 808 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and ComputeMgr::updateLocalComputes4().

zVector SimParameters::strainRate

Definition at line 556 of file SimParameters.h. Referenced by Controller::Controller().

zVector SimParameters::strainRate2

Definition at line 557 of file SimParameters.h. Referenced by Controller::Controller().

BigReal SimParameters::surface_tension

Definition at line 423 of file SimParameters.h. Referenced by ComputeLCPO::ComputeLCPO().

BigReal SimParameters::surfaceTensionTarget

Definition at line 545 of file SimParameters.h. Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and scriptSet().

Bool SimParameters::switchingActive

Definition at line 223 of file SimParameters.h. Referenced by ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

BigReal SimParameters::switchingDist

Definition at line 227 of file SimParameters.h. Referenced by ComputeNonbondedCUDA::recvYieldDevice(), and ComputeNonbondedUtil::select().

char SimParameters::symmetryFile[128]

Definition at line 357 of file SimParameters.h.

int SimParameters::symmetryFirstFullStep

Definition at line 359 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryFirstStep

Definition at line 359 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

BigReal SimParameters::symmetryk

Definition at line 355 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetrykfile[128]

Definition at line 356 of file SimParameters.h.

int SimParameters::symmetryLastFullStep

Definition at line 359 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryLastStep

Definition at line 359 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetryMatrixFile[128]

Definition at line 358 of file SimParameters.h.

Bool SimParameters::symmetryOn

Definition at line 354 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

Bool SimParameters::symmetryScaleForces

Definition at line 354 of file SimParameters.h. Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::tableInterpType[128]

Definition at line 340 of file SimParameters.h. Referenced by Parameters::read_ener_table().

BigReal SimParameters::tableMaxDist

Definition at line 342 of file SimParameters.h. Referenced by Parameters::read_ener_table().

int SimParameters::tableNumTypes

Definition at line 338 of file SimParameters.h. Referenced by Parameters::read_ener_table().

Real SimParameters::tableSpacing

Definition at line 341 of file SimParameters.h. Referenced by Parameters::read_ener_table().

Bool SimParameters::tabulatedEnergies

Definition at line 337 of file SimParameters.h. Referenced by Parameters::Parameters(), and ComputeNonbondedUtil::select().

char SimParameters::tabulatedEnergiesFile[128]

Definition at line 339 of file SimParameters.h. Referenced by Parameters::read_ener_table().

char SimParameters::tclBCArgs[128]

Definition at line 447 of file SimParameters.h. Referenced by ComputeTclBC::doWork(), and scriptSet().

Bool SimParameters::tclBCOn

Definition at line 445 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

char* SimParameters::tclBCScript

Definition at line 446 of file SimParameters.h. Referenced by ComputeTclBC::ComputeTclBC(), receive_SimParameters(), and send_SimParameters().

Bool SimParameters::tclForcesOn

Definition at line 441 of file SimParameters.h. Referenced by ComputeMgr::createComputes(), and Sequencer::integrate().

Bool SimParameters::tclIsThreaded

Definition at line 443 of file SimParameters.h. Referenced by ComputeTclBC::ComputeTclBC().

Bool SimParameters::tCoupleOn

Definition at line 474 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), NamdState::configListInit(), Molecule::receive_Molecule(), Molecule::send_Molecule(), Sequencer::tcoupleVelocities(), and Controller::tcoupleVelocities().

BigReal SimParameters::tCoupleTemp

Definition at line 476 of file SimParameters.h. Referenced by colvarproxy_namd::colvarproxy_namd(), and Controller::tcoupleVelocities().

Bool SimParameters::testOn

Definition at line 706 of file SimParameters.h.

Bool SimParameters::TMDDiffRMSD

Definition at line 346 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile[128]

Definition at line 348 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile2[128]

Definition at line 348 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDFinalRMSD

Definition at line 351 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDFirstStep

Definition at line 350 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDInitialRMSD

Definition at line 351 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDk

Definition at line 347 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDLastStep

Definition at line 350 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

Bool SimParameters::TMDOn

Definition at line 346 of file SimParameters.h. Referenced by ComputeMgr::createComputes().

int SimParameters::TMDOutputFreq

Definition at line 349 of file SimParameters.h. Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::totalAtoms

Definition at line 710 of file SimParameters.h.

int SimParameters::traceStartStep

Definition at line 140 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate().

int SimParameters::twoAwayX

Definition at line 162 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayY

Definition at line 163 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayZ

Definition at line 164 of file SimParameters.h. Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::useAntecedent

Definition at line 739 of file SimParameters.h.

Bool SimParameters::useCompressedPsf

Definition at line 782 of file SimParameters.h. Referenced by NamdState::configListInit(), and Molecule::Molecule().

Bool SimParameters::useConstantArea

Definition at line 525 of file SimParameters.h. Referenced by Controller::langevinPiston1(), and scriptSet().

Bool SimParameters::useConstantRatio

Definition at line 526 of file SimParameters.h. Referenced by Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().

Bool SimParameters::useDPME

Definition at line 595 of file SimParameters.h. Referenced by WorkDistrib::mapComputes().

Bool SimParameters::useFlexibleCell

Definition at line 524 of file SimParameters.h. Referenced by Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::receivePressure(), and scriptSet().

Bool SimParameters::useGroupPressure

Definition at line 519 of file SimParameters.h. Referenced by Sequencer::berendsenPressure(), Sequencer::langevinPiston(), Controller::receivePressure(), scriptSet(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

Bool SimParameters::useManyToMany

Definition at line 597 of file SimParameters.h. Referenced by OptPmeMgr::initialize().

int SimParameters::useNodeHelper

Definition at line 160 of file SimParameters.h. Referenced by PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), PmeXPencil::fft_init(), PmeZPencil::fft_init(), PmeXPencil::forward_fft(), PmeYPencil::forward_fft(), PmeZPencil::forward_fft(), PmeZPencil::send_all_ungrid(), PmeYPencil::send_trans(), PmeZPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), and Node::startup().

Bool SimParameters::useOptPME

Definition at line 596 of file SimParameters.h. Referenced by WorkDistrib::mapComputes(), and Node::startup().

int SimParameters::usePairlists

Definition at line 237 of file SimParameters.h. Referenced by Sequencer::runComputeObjects(), and SELF().

Bool SimParameters::usePluginIO

Definition at line 785 of file SimParameters.h. Referenced by NamdState::configListInit().

Bool SimParameters::useSettle

Definition at line 704 of file SimParameters.h. Referenced by HomePatch::rattle1(), and HomePatch::rattle2().

Bool SimParameters::vdwForceSwitching

Definition at line 225 of file SimParameters.h. Referenced by ComputeNonbondedUtil::select().

Bool SimParameters::vdwGeometricSigma

Definition at line 773 of file SimParameters.h.

BigReal SimParameters::vdwscale14

Definition at line 767 of file SimParameters.h. Referenced by NamdState::configListInit().

char SimParameters::velDcdFilename[128]

Definition at line 198 of file SimParameters.h.

int SimParameters::velDcdFrequency

Definition at line 190 of file SimParameters.h. Referenced by Output::velocity(), and Output::velocityNeeded().

int SimParameters::watmodel

Definition at line 109 of file SimParameters.h. Referenced by Molecule::num_deg_freedom(), HomePatch::rattle1(), HomePatch::rattle2(), and Sequencer::runComputeObjects().

Bool SimParameters::wrapAll

Definition at line 179 of file SimParameters.h. Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int().

Bool SimParameters::wrapNearest

Definition at line 180 of file SimParameters.h. Referenced by ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int().

Bool SimParameters::wrapWater

Definition at line 178 of file SimParameters.h. Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), and wrap_coor_int().

char SimParameters::xstFilename[128]

Definition at line 200 of file SimParameters.h. Referenced by Controller::outputExtendedSystem().

int SimParameters::xstFrequency

Definition at line 194 of file SimParameters.h. Referenced by Controller::outputExtendedSystem().

Bool SimParameters::zeroMomentum

Definition at line 176 of file SimParameters.h. Referenced by Sequencer::integrate(), and Controller::integrate().

Bool SimParameters::zeroMomentumAlt

Definition at line 177 of file SimParameters.h. Referenced by Sequencer::correctMomentum(), and Sequencer::submitMomentum().

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

• SimParameters.h
• SimParameters.C

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