NAMD: SimParameters Class Reference

Constructor & Destructor Documentation

SimParameters::SimParameters ( ) [inline]

Definition at line 864 of file SimParameters.h.

00864 : mgridforcelist() {};

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

Definition at line 865 of file SimParameters.h.

00865                                                  : mgridforcelist() {
00866           initialize_config_data(c,cwd);
00867         };

SimParameters::~SimParameters ( ) [inline]

Definition at line 868 of file SimParameters.h.

00868 {};

Member Function Documentation

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

Definition at line 94 of file SimParameters.C.

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

00096 {
00097 
00098    ParseOptions opts;   //  Object to check consistency of config file
00099 
00100    config_parser(opts);
00101 
00103    if (!opts.check_consistency()) 
00104    {
00105       NAMD_die("Internal error in configuration file parser");
00106    }
00107 
00108    // Now, feed the object with the actual configuration options through the
00109    // ParseOptions file and make sure everything is OK
00110    if (!opts.set(*config)) 
00111    {
00112       NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00113    }
00114 
00116 
00117    check_config(opts,config,cwd);
00118 
00119    print_config(opts,config,cwd);
00120 
00121 }

int SimParameters::isRecvSpanningTreeOn ( ) [inline]

Definition at line 886 of file SimParameters.h.

Referenced by Node::startup().

00886 { return proxyRecvSpanningTree == 1; }

int SimParameters::isSendSpanningTreeOn ( ) [inline]

Definition at line 884 of file SimParameters.h.

Referenced by Node::startup().

00884 { return proxySendSpanningTree == 1; }

void SimParameters::receive_SimParameters

(

MIStream *

)

Definition at line 6009 of file SimParameters.C.

References binAtomFile, binCoorFile, binRefFile, binVelFile, MGridforceParamsList::clear(), FFTWWisdomString, MIStream::get(), mgridforcelist, tclBCScript, and MGridforceParamsList::unpack_data().

06011 {
06012   msg->get(sizeof(SimParameters),(char*)this);
06013   if ( FFTWWisdomString ) {
06014     int fftwlen;
06015     msg->get(fftwlen);
06016     FFTWWisdomString = new char[fftwlen];
06017     msg->get(fftwlen,FFTWWisdomString);
06018 #ifdef NAMD_FFTW
06019 #ifdef NAMD_FFTW_3
06020     fftwf_import_wisdom_from_string(FFTWWisdomString);
06021 #else
06022     fftw_import_wisdom_from_string(FFTWWisdomString);
06023 #endif
06024 #endif
06025   }
06026   if ( tclBCScript ) {
06027     int tcllen;
06028     msg->get(tcllen);
06029     tclBCScript = new char[tcllen];
06030     msg->get(tcllen,tclBCScript);
06031   }
06032 
06033 #ifdef MEM_OPT_VERSION
06034   int filelen;
06035   msg->get(filelen);
06036   binAtomFile = new char[filelen];
06037   msg->get(filelen, binAtomFile);
06038   
06039   msg->get(filelen);
06040   binCoorFile = new char[filelen];
06041   msg->get(filelen, binCoorFile);
06042 
06043   if(binVelFile) {    
06044     msg->get(filelen);
06045     binVelFile = new char[filelen];
06046     msg->get(filelen, binVelFile);
06047   }
06048 
06049   if(binRefFile) {    
06050     msg->get(filelen);
06051     binRefFile = new char[filelen];
06052     msg->get(filelen, binRefFile);
06053   }
06054 #endif
06055 
06056 
06057   // The simParameters bit copy above put illegal values in the list pointers
06058   // So this resets everything so that unpacking will work.
06059   mgridforcelist.clear();
06060   mgridforcelist.unpack_data(msg);
06061   
06062   delete msg;
06063 }

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

Definition at line 135 of file SimParameters.C.

References accelMDalpha, accelMDE, accelMDTalpha, accelMDTE, alchDispLambda, alchElecLambda, alchEquilSteps, alchFepElecOn, alchFepWCADispOn, alchFepWCArcut1, alchFepWCArcut2, alchFepWCArcut3, alchFepWCARepuOn, alchLambda, alchLambda2, alchRepLambda, atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, commOnly, consForceScaling, constraintScaling, eField, eFieldFreq, eFieldPhase, firstTimestep, fixCellDims, fixCellDimX, fixCellDimY, fixCellDimZ, fixedAtomsOn, initialTemp, langevin_useBAOAB, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, maximumMove, minimizeOn, 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().

00135                                                                   {
00136 
00137   if ( CkMyRank() ) return;
00138 
00139 #define MAX_SCRIPT_PARAM_SIZE 128
00140 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00141 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00142 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00143 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
00144 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00145 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00146 
00147   SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00148   SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00149   SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00150   SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00151   SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00152   SCRIPT_PARSE_INT("numsteps",N)
00153   SCRIPT_PARSE_INT("firsttimestep",firstTimestep)
00154   SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00155   SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00156   SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
00157   SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
00158   // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00159   SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00160   SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
00161   SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
00162   SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00163   SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00164   SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00165   SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00166   SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
00167   SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
00168   SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
00169   SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
00170   SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00171   SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00172   SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
00173                         langevinPistonTarget,/PRESSUREFACTOR)
00174   SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00175   SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00176   SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00177   SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
00178                         surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
00179   SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00180   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
00181                         berendsenPressureTarget,/PRESSUREFACTOR)
00182   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
00183                         berendsenPressureCompressibility,*PRESSUREFACTOR)
00184   SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00185                                 berendsenPressureRelaxationTime)
00186   SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00187   SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00188   SCRIPT_PARSE_STRING("outputname",outputFilename)
00189   SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00190   SCRIPT_PARSE_VECTOR("eField",eField)
00191   SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00192   SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
00193   SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 
00194   SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 
00195   SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 
00196   SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 
00197   SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00198   SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00199   if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
00200     NAMD_die("Can't yet modify mgridforcescale in a script");
00201     return;
00202   }
00203   if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
00204     NAMD_die("Can't yet modify mgridforcevoff in a script");
00205     return;
00206   }
00207    
00208   if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00209     if ( ! fixedAtomsOn )
00210       NAMD_die("FixedAtoms may not be enabled in a script.");
00211     if ( ! fixedAtomsForces )
00212       NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00213     fixedAtomsOn = atobool(value);
00214     return;
00215   }
00216 
00217 //Modifications for alchemical fep
00218   SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
00219 
00220   if ( ! strncasecmp(param,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00221     alchRepLambda = atof(value);
00222     alchFepWCARepuOn = true;
00223     alchFepWCADispOn = false;
00224     alchFepElecOn    = false;
00225     ComputeNonbondedUtil::select();
00226     return;
00227   }
00228 
00229   if ( ! strncasecmp(param,"alchDispLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00230     alchDispLambda = atof(value);
00231     alchFepWCARepuOn = false;
00232     alchFepWCADispOn = true;
00233     alchFepElecOn    = false;
00234     ComputeNonbondedUtil::select();
00235     return;
00236   }
00237 
00238   if ( ! strncasecmp(param,"alchElecLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00239     alchElecLambda = atof(value);
00240     alchFepWCARepuOn = false;
00241     alchFepWCADispOn = false;
00242     alchFepElecOn    = true;
00243     ComputeNonbondedUtil::select();
00244     return;
00245   }
00246 
00247 
00248   if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) {
00249     alchFepWCArcut1 = atof(value);
00250     ComputeNonbondedUtil::select();
00251     return;
00252   }
00253 
00254   if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) {
00255     alchFepWCArcut2 = atof(value);
00256     ComputeNonbondedUtil::select();
00257     return;
00258   }
00259 
00260   if ( ! strncasecmp(param,"alchFepWCArcut3",MAX_SCRIPT_PARAM_SIZE) ) {
00261     alchFepWCArcut3 = atof(value);
00262     ComputeNonbondedUtil::select();
00263     return;
00264   }
00265 
00266   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00267     alchLambda = atof(value);
00268     ComputeNonbondedUtil::select();
00269     return;
00270   }
00271 
00272   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00273     alchLambda2 = atof(value);
00274     ComputeNonbondedUtil::select();
00275     return;
00276   }
00277 //fepe
00278 
00279 // REDUNDANT TI BEGINS
00280 //  if ( ! strncasecmp(param,"tiLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00281 //    alchLambda = atof(value);
00282 //    ComputeNonbondedUtil::select();
00283 //    return;
00284 //  }
00285 // REDUNDANT TI ENDS
00286 
00287   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00288     nonbondedScaling = atof(value);
00289     ComputeNonbondedUtil::select();
00290     return;
00291   }
00292   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00293     commOnly = atobool(value);
00294     ComputeNonbondedUtil::select();
00295     return;
00296   }
00297 
00298   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00299   sprintf(error,"Setting parameter %s from script failed!\n",param);
00300   NAMD_die(error);
00301 
00302 }

void SimParameters::send_SimParameters

(

MOStream *

)

Definition at line 5951 of file SimParameters.C.

References binAtomFile, binCoorFile, binRefFile, binVelFile, MOStream::end(), FFTWWisdomString, mgridforcelist, MGridforceParamsList::pack_data(), MOStream::put(), and tclBCScript.

05953 {
05954   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
05955   if ( msg == NULL )
05956   {
05957     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
05958   }*/
05959 
05960   msg->put(sizeof(SimParameters),(char*)this);
05961   if ( FFTWWisdomString ) {
05962     int fftwlen = strlen(FFTWWisdomString) + 1;
05963     msg->put(fftwlen);
05964     msg->put(fftwlen,FFTWWisdomString);
05965   }
05966   if ( tclBCScript ) {
05967     int tcllen = strlen(tclBCScript) + 1;
05968     msg->put(tcllen);
05969     msg->put(tcllen,tclBCScript);
05970   }
05971 
05972 #ifdef MEM_OPT_VERSION
05973   int filelen = strlen(binAtomFile)+1;
05974   msg->put(filelen);
05975   msg->put(filelen, binAtomFile);
05976 
05977   filelen = strlen(binCoorFile)+1;
05978   msg->put(filelen);
05979   msg->put(filelen, binCoorFile);
05980 
05981   if(binVelFile) {
05982     filelen = strlen(binVelFile)+1;
05983     msg->put(filelen);
05984     msg->put(filelen, binVelFile);
05985   }
05986 
05987   if(binRefFile) {
05988     filelen = strlen(binRefFile)+1;
05989     msg->put(filelen);
05990     msg->put(filelen, binRefFile);
05991   }
05992 #endif
05993 
05994   mgridforcelist.pack_data(msg);
05995   
05996   msg->end();
05997 }

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
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	useCkLoop
int	twoAwayX
int	twoAwayY
int	twoAwayZ
int	maxPatches
Bool	ldbUnloadPME
Bool	ldbUnloadZero
Bool	ldbUnloadOne
Bool	ldbUnloadOutputPEs
Bool	noPatchesOnZero
Bool	noPatchesOnOutputPEs
Bool	noPatchesOnOne
BigReal	initialTemp
Bool	comMove
Bool	zeroMomentum
Bool	zeroMomentumAlt
Bool	wrapWater
Bool	wrapAll
Bool	wrapNearest
BigReal	dielectric
ExclusionSettings	exclude
BigReal	scale14
BigReal	nonbondedScaling
int	dcdFrequency
int	dcdUnitCell
int	velDcdFrequency
int	forceDcdFrequency
int	xstFrequency
char	auxFilename [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
Bool	sphericalConstraintsOn
zVector	sphericalConstrCenter
BigReal	constraintScaling
Bool	paraTypeXplorOn
Bool	paraTypeCharmmOn
Bool	goGroPair
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
Bool	alchFepElecOn
Bool	alchFepWhamOn
int	alchMethod
BigReal	alchLambda
BigReal	alchLambda2
BigReal	alchRepLambda
BigReal	alchDispLambda
BigReal	alchElecLambda
BigReal	alchFepWCArcut1
BigReal	alchFepWCArcut2
BigReal	alchFepWCArcut3
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
Bool	drudeHardWallOn
BigReal	drudeTemp
BigReal	drudeDamping
BigReal	drudeBondLen
BigReal	drudeBondConst
BigReal	drudeNbtholeCut
Bool	pairInteractionOn
int	pairInteractionGroup1
int	pairInteractionGroup2
Bool	pairInteractionSelf
Bool	cosAngles
Bool	globalForcesOn
Bool	tclForcesOn
Bool	tclIsThreaded
Bool	tclBCOn
char *	tclBCScript
char	tclBCArgs [128]
Bool	freeEnergyOn
Bool	miscForcesOn
Bool	colvarsOn
Bool	fixedAtomsOn
Bool	fixedAtomsForces
Bool	langevinOn
BigReal	langevinTemp
BigReal	langevinDamping
Bool	langevinHydrogen
Bool	langevin_useBAOAB
Bool	loweAndersenOn
BigReal	loweAndersenTemp
BigReal	loweAndersenRate
BigReal	loweAndersenCutoff
Bool	globalOn
Bool	dihedralOn
Bool	COLDOn
BigReal	COLDRate
BigReal	COLDTemp
Bool	tCoupleOn
BigReal	tCoupleTemp
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
Bool	langevinPistonBarrier
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	MSMQuality
int	MSMApprox
int	MSMSplit
int	MSMLevels
int	MSMBlockSizeX
int	MSMBlockSizeY
int	MSMBlockSizeZ
BigReal	MSMGridSpacing
BigReal	MSMPadding
Bool	MsmSerialOn
Bool	FMMOn
int	FMMLevels
BigReal	FMMPadding
Bool	PMEOn
BigReal	PMETolerance
BigReal	PMEEwaldCoefficient
int	PMEInterpOrder
int	PMEGridSizeX
int	PMEGridSizeY
int	PMEGridSizeZ
BigReal	PMEGridSpacing
int	PMEProcessors
int	PMEMinSlices
int	PMEMinPoints
Bool	PMEBarrier
int	PMEPencils
int	PMEPencilsX
int	PMEPencilsY
int	PMEPencilsZ
int	PMEPencilsYLayout
int	PMEPencilsXLayout
int	PMESendOrder
Bool	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
Bool	ignoreMass
int	splitPatch
BigReal	hgroupCutoff
int	mollyOn
BigReal	mollyTol
int	mollyIter
int	rigidBonds
BigReal	rigidTol
int	rigidIter
int	rigidDie
Bool	useSettle
Bool	testOn
Bool	commOnly
Bool	statsOn
int	totalAtoms
int	maxSelfPart
int	maxPairPart
int	numAtomsSelf
int	numAtomsSelf2
int	numAtomsPair
int	numAtomsPair2
int	minAtomsPerPatch
int	maxExclusionFlags
Bool	outputPatchDetails
Bool	staticAtomAssignment
Bool	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
char *	binRefFile
int	numoutputprocs
int	numoutputwrts
char	computeMapFilename [128]
Bool	storeComputeMap
Bool	loadComputeMap