NAMD: SimParameters Class Reference

00119                                                                   {
00120 
00121 #define MAX_SCRIPT_PARAM_SIZE 128
00122 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00123 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00124 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00125 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
00126 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00127 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00128 
00129   SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00130   SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00131   SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00132   SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00133   SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00134   SCRIPT_PARSE_INT("numsteps",N)
00135   SCRIPT_PARSE_INT("firsttimestep",firstTimestep)
00136   SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00137   SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00138   // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00139   SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00140   SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00141   SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00142   SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00143   SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00144   SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
00145   SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
00146   SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
00147   SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
00148   SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00149   SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00150   SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
00151                         langevinPistonTarget,/PRESSUREFACTOR)
00152   SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00153   SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00154   SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00155   SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
00156                         surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
00157   SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00158   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
00159                         berendsenPressureTarget,/PRESSUREFACTOR)
00160   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
00161                         berendsenPressureCompressibility,*PRESSUREFACTOR)
00162   SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00163                                 berendsenPressureRelaxationTime)
00164   SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00165   SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00166   SCRIPT_PARSE_STRING("outputname",outputFilename)
00167   SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00168   SCRIPT_PARSE_VECTOR("eField",eField)
00169   SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00170   SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
00171   SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00172   SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00173   if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
00174     NAMD_die("Can't yet modify mgridforcescale in a script");
00175     return;
00176   }
00177   if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
00178     NAMD_die("Can't yet modify mgridforcevoff in a script");
00179     return;
00180   }
00181    
00182   if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00183     if ( ! fixedAtomsOn )
00184       NAMD_die("FixedAtoms may not be enabled in a script.");
00185     if ( ! fixedAtomsForces )
00186       NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00187     fixedAtomsOn = atobool(value);
00188     return;
00189   }
00190 
00191 //Modifications for alchemical fep
00192   SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
00193 
00194   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00195     alchLambda = atof(value);
00196     ComputeNonbondedUtil::select();
00197     return;
00198   }
00199 
00200   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00201     alchLambda2 = atof(value);
00202     ComputeNonbondedUtil::select();
00203     return;
00204   }
00205 //fepe
00206 
00207 // REDUNDANT TI BEGINS
00208 //  if ( ! strncasecmp(param,"tiLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00209 //    alchLambda = atof(value);
00210 //    ComputeNonbondedUtil::select();
00211 //    return;
00212 //  }
00213 // REDUNDANT TI ENDS
00214 
00215   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00216     nonbondedScaling = atof(value);
00217     ComputeNonbondedUtil::select();
00218     return;
00219   }
00220   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00221     commOnly = atobool(value);
00222     ComputeNonbondedUtil::select();
00223     return;
00224   }
00225 
00226   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00227   sprintf(error,"Setting parameter %s from script failed!\n",param);
00228   NAMD_die(error);
00229 
00230 }

SimParameters Class Reference

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation


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
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	ldbStrategy
int	ldbPeriod
int	firstLdbStep
int	lastLdbStep
BigReal	ldbBackgroundScaling
BigReal	ldbPMEBackgroundScaling
BigReal	ldbHomeBackgroundScaling
int	twoAwayX
int	twoAwayY
int	twoAwayZ
Bool	ldbUnloadPME
Bool	ldbUnloadSMP
Bool	ldbUnloadZero
Bool	ldbUnloadOne
Bool	ldbUnloadRankZero
int	procsPerNode
int	ldbUnloadRank
Bool	noPatchesOnZero
Bool	noPatchesOnOne
Bool	shiftIOToOne
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	xstFrequency
char	auxFilename [128]
char	dcdFilename [128]
char	velDcdFilename [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
BigReal	switchingDist
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	mgridforceOn
MGridforceParamsList	mgridforcelist
Bool	selectConstraintsOn
Bool	constrXOn
Bool	constrYOn
Bool	constrZOn
BigReal	constraintScaling
Bool	paraTypeXplorOn
Bool	paraTypeCharmmOn
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
BigReal	TMDk
char	TMDFile [128]
int	TMDOutputFreq
int	TMDFirstStep
int	TMDLastStep
BigReal	TMDInitialRMSD
BigReal	TMDFinalRMSD
Bool	alchOn
Bool	alchFepOn
Bool	alchThermIntOn
int	alchMethod
BigReal	alchLambda
BigReal	alchLambda2
BigReal	alchTemp
int	alchOutFreq
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	drudeOn
BigReal	drudeTemp
Bool	pairInteractionOn
int	pairInteractionGroup1
int	pairInteractionGroup2
Bool	pairInteractionSelf
Bool	cosAngles
Bool	globalForcesOn
Bool	tclForcesOn
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	globalOn
Bool	dihedralOn
Bool	COLDOn
BigReal	COLDRate
BigReal	COLDTemp
Bool	tCoupleOn
BigReal	tCoupleTemp
int	rescaleFreq
BigReal	rescaleTemp
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	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	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
int	totalAtoms
int	maxSelfPart
int	maxPairPart
int	numAtomsSelf
int	numAtomsSelf2
int	numAtomsPair
int	numAtomsPair2
int	minAtomsPerPatch
int	maxExclusionFlags
Bool	outputPatchDetails
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
int	proxySendSpanningTree
int	proxyRecvSpanningTree