SimParameters Class Reference

#include <SimParameters.h>

List of all members.

Public Member Functions

BigReal getCurrentLambda (const int)
BigReal getCurrentLambda2 (const int)
BigReal getLambdaDelta (void)
BigReal getElecLambda (const BigReal)
BigReal getVdwLambda (const BigReal)
BigReal getBondLambda (const BigReal)
 SimParameters ()
 SimParameters (ConfigList *c, char *&cwd)
 ~SimParameters ()
void initialize_config_data (ConfigList *, char *&cwd)
void send_SimParameters (MOStream *)
void receive_SimParameters (MIStream *)
void scriptSet (const char *, const char *)
void close_dcdfile ()
void close_veldcdfile ()
int isSendSpanningTreeOn ()
int isSendSpanningTreeUnset ()
int isRecvSpanningTreeOn ()
int isRecvSpanningTreeUnset ()
char * getfromparseopts (const char *name, char *outbuf)
int istrueinparseopts (const char *name)
int issetinparseopts (const char *name)
void readExtendedSystem (const char *filename, Lattice *latptr=0)

Static Public Member Functions

static void nonbonded_select ()
static void pme_select ()

Public Attributes

Bool lonepairs
int watmodel
Bool LJcorrection
BigReal dt
int N
int stepsPerCycle
zVector cellBasisVector1
zVector cellBasisVector2
zVector cellBasisVector3
zVector cellOrigin
Lattice lattice
int nonbondedFrequency
int fullElectFrequency
BigReal fmaTheta
int ldBalancer
int ldbStrategy
int ldbPeriod
int firstLdbStep
int lastLdbStep
int hybridGroupSize
BigReal ldbBackgroundScaling
BigReal ldbPMEBackgroundScaling
BigReal ldbHomeBackgroundScaling
BigReal ldbRelativeGrainsize
int traceStartStep
int numTraceSteps
Bool outputMaps
Bool simulateInitialMapping
int simulatedPEs
int simulatedNodeSize
Bool disableTopology
Bool verboseTopology
Bool benchTimestep
int useCkLoop
int twoAwayX
int twoAwayY
int twoAwayZ
int maxPatches
Bool ldbUnloadPME
Bool ldbUnloadZero
Bool ldbUnloadOne
Bool ldbUnloadOutputPEs
Bool noPatchesOnZero
Bool noPatchesOnOutputPEs
Bool noPatchesOnOne
BigReal initialTemp
Bool comMove
Bool zeroMomentum
Bool zeroMomentumAlt
Bool wrapWater
Bool wrapAll
Bool wrapNearest
BigReal dielectric
ExclusionSettings exclude
BigReal scale14
BigReal nonbondedScaling
int dcdFrequency
int dcdUnitCell
int velDcdFrequency
int forceDcdFrequency
int xstFrequency
char auxFilename [128]
char dcdFilename [128]
char velDcdFilename [128]
char forceDcdFilename [128]
char xstFilename [128]
char outputFilename [128]
char restartFilename [128]
int restartFrequency
Bool restartSave
Bool restartSaveDcd
Bool binaryRestart
Bool binaryOutput
BigReal cutoff
BigReal margin
BigReal patchDimension
BigReal limitDist
Bool switchingActive
Bool vdwForceSwitching
BigReal switchingDist
Bool martiniSwitching
Bool martiniDielAllow
BigReal pairlistDist
int pairlistMinProcs
int usePairlists
int pairlistsPerCycle
BigReal pairlistShrink
BigReal pairlistGrow
BigReal pairlistTrigger
int outputPairlists
Bool constraintsOn
int constraintExp
Bool gridforceOn
Bool gridforceVolts
zVector gridforceScale
Bool gridforceContA1
Bool gridforceContA2
Bool gridforceContA3
zVector gridforceVOffset
Bool gridforceLite
Bool gridforcechecksize
Bool mgridforceOn
MGridforceParamsList mgridforcelist
Bool selectConstraintsOn
Bool constrXOn
Bool constrYOn
Bool constrZOn
Bool sphericalConstraintsOn
zVector sphericalConstrCenter
BigReal constraintScaling
Bool paraTypeXplorOn
Bool paraTypeCharmmOn
Bool goGroPair
Bool goForcesOn
char goParameters [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 alchOnAtStartup
Bool alchFepOnAtStartup
Bool alchThermIntOnAtStartup
Bool alchOn
Bool alchFepOn
Bool alchThermIntOn
Bool alchFepWCARepuOn
Bool alchFepWCADispOn
Bool alchFepElecOn
Bool alchFepWhamOn
int alchMethod
BigReal alchLambda
BigReal alchLambda2
BigReal alchLambdaIDWS
int alchIDWSfreq
int alchLambdaFreq
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
BigReal alchBondLambdaEnd
Bool alchDecouple
Bool alchBondDecouple
Bool lesOn
int lesFactor
Bool lesReduceTemp
Bool lesReduceMass
Bool soluteScalingOn
BigReal soluteScalingFactor
BigReal soluteScalingFactorCharge
BigReal soluteScalingFactorVdw
Bool soluteScalingAll
Bool extForcesOn
char extForcesCommand [256]
char extCoordFilename [128]
char extForceFilename [128]
Bool qmForcesOn
char qmParamPDB [128]
Bool qmParamPDBDefined
Bool qmChrgFromPSF
char qmExecPath [256]
char qmSoftware [128]
char qmChrgModeS [16]
int qmChrgMode
char qmColumn [16]
char qmBaseDir [256]
char qmSecProc [256]
Bool qmSecProcOn
char qmPrepProc [256]
Bool qmPrepProcOn
int qmFormat
Bool qmReplaceAll
Bool qmMOPACAddConfigChrg
Bool qmBondOn
char qmBondColumn [16]
Bool qmBondDist
int qmBondValType
char qmBondValueTypeS [16]
char qmBondSchemeS [16]
int qmBondScheme
Bool qmPCSwitchOn
char qmPCSwitchTypeS [16]
int qmPCSwitchType
char qmPCSchemeS [16]
int qmPCScheme
int qmSimsPerNode
Bool qmVDW
Bool qmNoPC
Bool qmElecEmbed
int qmPCSelFreq
Bool qmCustomPCSel
Bool qmLSSOn
int qmLSSFreq
char qmLSSResname [5]
char qmLSSModeS [16]
int qmLSSMode
Bool qmCSMD
char qmCSMDFile [128]
int qmEnergyOutFreq
int qmOutFreq
int qmPosOutFreq
Bool printBadContacts
Bool GBISOn
BigReal fsMax
Bool GBISserOn
BigReal solvent_dielectric
BigReal coulomb_radius_offset
BigReal kappa
BigReal ion_concentration
BigReal gbis_delta
BigReal gbis_beta
BigReal gbis_gamma
BigReal alpha_cutoff
BigReal alpha_max
Bool LCPOOn
BigReal surface_tension
Bool drudeOn
Bool drudeHardWallOn
BigReal drudeTemp
BigReal drudeDamping
BigReal drudeBondLen
BigReal drudeBondConst
BigReal drudeNbtholeCut
Bool pairInteractionOn
int pairInteractionGroup1
int pairInteractionGroup2
Bool pairInteractionSelf
Bool cosAngles
Bool globalForcesOn
Bool tclForcesOn
Bool tclIsThreaded
Bool tclBCOn
char * tclBCScript
char tclBCArgs [128]
Bool freeEnergyOn
Bool miscForcesOn
Bool colvarsOn
Bool fixedAtomsOn
Bool fixedAtomsForces
Bool fixedAtomsForceOutput
Bool langevinOnAtStartup
Bool langevinOn
BigReal langevinTemp
BigReal langevinDamping
Bool langevinHydrogen
Bool langevin_useBAOAB
Bool loweAndersenOn
BigReal loweAndersenTemp
BigReal loweAndersenRate
BigReal loweAndersenCutoff
Bool globalOn
Bool dihedralOn
Bool COLDOn
BigReal COLDRate
BigReal COLDTemp
Bool tCoupleOn
BigReal tCoupleTemp
Bool stochRescaleOn
BigReal stochRescaleTemp
BigReal stochRescalePeriod
int stochRescaleFreq
int rescaleFreq
BigReal rescaleTemp
Bool accelMDOn
Bool accelMDdihe
Bool accelMDdual
Bool accelMDDebugOn
BigReal accelMDFirstStep
BigReal accelMDLastStep
int accelMDOutFreq
BigReal accelMDE
BigReal accelMDalpha
BigReal accelMDTE
BigReal accelMDTalpha
Bool accelMDG
int accelMDGiE
int accelMDGcMDSteps
int accelMDGEquiSteps
int accelMDGcMDPrepSteps
int accelMDGEquiPrepSteps
BigReal accelMDGSigma0P
BigReal accelMDGSigma0D
Bool accelMDGRestart
char accelMDGRestartFile [128]
Bool accelMDGresetVaftercmd
Bool adaptTempOn
Bool adaptTempDebug
int adaptTempFirstStep
int adaptTempLastStep
int adaptTempOutFreq
int adaptTempFreq
BigReal adaptTempTmin
BigReal adaptTempTmax
BigReal adaptTempAutoDt
int adaptTempBins
BigReal adaptTempDt
BigReal adaptTempCgamma
Bool adaptTempLangevin
Bool adaptTempRescale
char adaptTempInFile [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
Bool multigratorOn
BigReal multigratorPressureTarget
BigReal multigratorPressureRelaxationTime
int multigratorPressureFreq
BigReal multigratorTemperatureTarget
BigReal multigratorTemperatureRelaxationTime
int multigratorTemperatureFreq
int multigratorNoseHooverChainLength
BigReal surfaceTensionTarget
Bool pressureProfileOn
int pressureProfileSlabs
int pressureProfileFreq
int pressureProfileAtomTypes
Bool pressureProfileEwaldOn
int pressureProfileEwaldX
int pressureProfileEwaldY
int pressureProfileEwaldZ
zVector strainRate
zVector strainRate2
unsigned int randomSeed
Bool FMAOn
int FMALevels
int FMAMp
Bool FMAFFTOn
int FMAFFTBlock
Bool fullDirectOn
Bool MSMOn
int MSMQuality
int MSMApprox
int MSMSplit
int MSMLevels
int MSMBlockSizeX
int MSMBlockSizeY
int MSMBlockSizeZ
BigReal MSMGridSpacing
BigReal MSMPadding
BigReal MSMxmin
BigReal MSMxmax
BigReal MSMymin
BigReal MSMymax
BigReal MSMzmin
BigReal MSMzmax
Bool MsmSerialOn
Bool FMMOn
int FMMLevels
BigReal FMMPadding
Bool PMEOn
BigReal PMETolerance
BigReal PMEEwaldCoefficient
int PMEInterpOrder
int PMEGridSizeX
int PMEGridSizeY
int PMEGridSizeZ
BigReal PMEGridSpacing
int PMEProcessors
int PMEMinSlices
int PMEMinPoints
Bool PMEBarrier
int PMEPencils
int PMEPencilsX
int PMEPencilsY
int PMEPencilsZ
int PMEPencilsYLayout
int PMEPencilsXLayout
int PMESendOrder
Bool PMEOffload
Bool useDPME
Bool usePMECUDA
Bool useCUDA2
int bondedCUDA
Bool useCUDAdisable
Bool 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
Bool eFieldNormalized
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 replicaUniformPatchGrids
Bool HydrogenBonds
Bool useAntecedent
int aaAngleExp
int haAngleExp
int distAttExp
int distRepExp
BigReal dhaCutoffAngle
BigReal dhaOnAngle
BigReal dhaOffAngle
BigReal daCutoffDist
BigReal daOnDist
BigReal daOffDist
int IMDon
int IMDport
int IMDfreq
int IMDwait
int IMDignore
int IMDignoreForces
Bool amberOn
Bool readExclusions
BigReal vdwscale14
Bool gromacsOn
Bool vdwGeometricSigma
BigReal scriptArg1
BigReal scriptArg2
BigReal scriptArg3
BigReal scriptArg4
BigReal scriptArg5
int scriptIntArg1
int scriptIntArg2
char scriptStringArg1 [128]
char scriptStringArg2 [128]
Bool useCompressedPsf
Bool genCompressedPsf
Bool usePluginIO
Bool mallocTest
Bool printExclusions
int proxySendSpanningTree
int proxyRecvSpanningTree
int proxyTreeBranchFactor
int numinputprocs
char * binAtomFile
char * binCoorFile
char * binVelFile
char * binRefFile
int numoutputprocs
int numoutputwrts
char computeMapFilename [128]
Bool storeComputeMap
Bool loadComputeMap
int mic_hostSplit
int mic_numParts_self_p1
int mic_numParts_pair_p1
int mic_numParts_pair_p2
int mic_unloadMICPEs
int mic_deviceThreshold
int mic_singleKernel


Detailed Description

Definition at line 100 of file SimParameters.h.


Constructor & Destructor Documentation

SimParameters::SimParameters (  )  [inline]

Definition at line 1037 of file SimParameters.h.

01037 : mgridforcelist(), parseopts(0) {};

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

Definition at line 1038 of file SimParameters.h.

References initialize_config_data().

01038                                                  : mgridforcelist(), parseopts(0) {
01039           initialize_config_data(c,cwd);
01040         };

SimParameters::~SimParameters (  )  [inline]

Definition at line 1041 of file SimParameters.h.

01041 {};


Member Function Documentation

void SimParameters::close_dcdfile (  ) 

Definition at line 655 of file Output.C.

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

Referenced by scriptSet().

00655                                   {
00656 
00657   Output *output = Node::Object()->output;
00658   if ( ! output ) return;
00659 
00660   output->output_dcdfile(END_OF_RUN, 0, 0, 0);
00661 
00662 }

void SimParameters::close_veldcdfile (  ) 

Definition at line 664 of file Output.C.

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

Referenced by scriptSet().

00664                                      {
00665 
00666   Output *output = Node::Object()->output;
00667   if ( ! output ) return;
00668 
00669   output->output_veldcdfile(END_OF_RUN, 0, 0);
00670 
00671 }

BigReal SimParameters::getBondLambda ( const   BigReal  ) 

Definition at line 7221 of file SimParameters.C.

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

07221                                                          {
07222   // Convenience function for staggered lambda scaling
07223   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
07224 }

BigReal SimParameters::getCurrentLambda ( const   int  ) 

Definition at line 7168 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, firstTimestep, and getLambdaDelta().

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

07168                                                       {
07169   /*Get lambda at the current step. 
07170 
07171    If alchLambdaFreq = 0, return alchLambda. For positive values of 
07172    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
07173    alchLambda2:
07174 
07175    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
07176 
07177    n - the current time step
07178    n0 - step at which switching begins (default = 0)
07179    N - total steps in the simulation
07180    dn - alchLambdaFreq (increment frequency, in steps)
07181    l/l2 - alchLambda/alchLambda2
07182  
07183    Note that each step _begins_ by incrementing alchLambda and then integrates
07184    in time. This means that the first and last switch steps may not behave as
07185    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
07186    no step occurs because alchLambda2 has already been reached.
07187   */
07188   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
07189     if ( step == N ) {
07190       return alchLambda2;
07191     }
07192     else {
07193       const int timeOrigin = firstTimestep + alchEquilSteps;
07194       const BigReal alchLambdaDelta = getLambdaDelta();
07195       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
07196       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
07197     }
07198   }
07199   else {
07200     return alchLambda;
07201   }
07202 }

BigReal SimParameters::getCurrentLambda2 ( const   int  ) 

Definition at line 7156 of file SimParameters.C.

References alchIDWSfreq, and alchLambdaIDWS.

Referenced by Controller::outputTiEnergy().

07156                                                        {
07157   if ( alchLambdaIDWS >= 0. ) {
07158     const BigReal lambda2 = ( (step / alchIDWSfreq) % 2 == 1 ) ? alchLambda2 : alchLambdaIDWS;
07159     return lambda2;
07160   } else {
07161     return alchLambda2;
07162   }
07163 }

BigReal SimParameters::getElecLambda ( const   BigReal  ) 

Definition at line 7210 of file SimParameters.C.

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

07210                                                          {
07211   // Convenience function for staggered lambda scaling
07212   return (lambda <= alchElecLambdaStart ? 0.
07213           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
07214 }

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

Definition at line 99 of file SimParameters.C.

References ParseOptions::getfromptr().

00099                                                                     {
00100   if ( parseopts ) return parseopts->getfromptr(name,outbuf);
00101   else return 0;
00102 }

BigReal SimParameters::getLambdaDelta ( void   ) 

Definition at line 7204 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, and firstTimestep.

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

07204                                           {
07205   // Increment by which Lambda changes.
07206   return ((alchLambda2 - alchLambda)*alchLambdaFreq
07207           / BigReal(N - firstTimestep - alchEquilSteps));
07208 }

BigReal SimParameters::getVdwLambda ( const   BigReal  ) 

Definition at line 7216 of file SimParameters.C.

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

07216                                                         {
07217   // Convenience function for staggered lambda scaling
07218   return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
07219 }

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

Definition at line 127 of file SimParameters.C.

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

Referenced by SimParameters().

00129 {
00130 
00131    parseopts = new ParseOptions;   //  Object to check consistency of config file
00132    ParseOptions &opts = *parseopts;
00133 
00134    config_parser(opts);
00135 
00137    if (!opts.check_consistency()) 
00138    {
00139       NAMD_die("Internal error in configuration file parser");
00140    }
00141 
00142    // Now, feed the object with the actual configuration options through the
00143    // ParseOptions file and make sure everything is OK
00144    if (!opts.set(*config)) 
00145    {
00146       NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00147    }
00148 
00150 
00151    check_config(opts,config,cwd);
00152 
00153    print_config(opts,config,cwd);
00154 
00155 }

int SimParameters::isRecvSpanningTreeOn (  )  [inline]

Definition at line 1063 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

01063 { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (  )  [inline]

Definition at line 1064 of file SimParameters.h.

References proxyRecvSpanningTree.

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

01064 { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (  )  [inline]

Definition at line 1061 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

01061 { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (  )  [inline]

Definition at line 1062 of file SimParameters.h.

References proxySendSpanningTree.

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

01062 { return proxySendSpanningTree == -1; }

int SimParameters::issetinparseopts ( const char *  name  ) 

Definition at line 109 of file SimParameters.C.

References ParseOptions::issetfromptr().

00109                                                     {
00110   if ( parseopts ) return parseopts->issetfromptr(name);
00111   else return -1;
00112 }

int SimParameters::istrueinparseopts ( const char *  name  ) 

Definition at line 104 of file SimParameters.C.

References ParseOptions::istruefromptr().

00104                                                      {
00105   if ( parseopts ) return parseopts->istruefromptr(name);
00106   else return -1;
00107 }

void SimParameters::nonbonded_select (  )  [static]

Definition at line 446 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

00446                                      {
00447     ComputeNonbondedUtil::select();
00448 }

void SimParameters::pme_select (  )  [static]

Definition at line 450 of file SimParameters.C.

References ComputePmeUtil::select().

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

00450                                {
00451   ComputePmeUtil::select();
00452 }

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

Definition at line 2367 of file SimParameters.C.

References Lattice::a_p(), Lattice::b_p(), Lattice::c_p(), cellBasisVector1, cellBasisVector2, cellBasisVector3, cellOrigin, endi(), if(), iINFO(), iout, lattice, NAMD_die(), strainRate, strainRate2, Vector::x, Vector::y, and Vector::z.

02367                                                                             {
02368 
02369      if ( ! latptr ) {
02370        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
02371      }
02372 
02373      ifstream xscFile(filename);
02374      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
02375 
02376      char labels[1024];
02377      do {
02378        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02379        xscFile.getline(labels,1023);
02380      } while ( strncmp(labels,"#$LABELS ",9) );
02381 
02382      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
02383      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
02384      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
02385      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
02386 
02387      int pos = 0;
02388      char *l_i = labels + 8;
02389      while ( *l_i ) {
02390        if ( *l_i == ' ' ) { ++l_i; continue; }
02391        char *l_i2;
02392        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
02393        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
02394          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
02395          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
02396          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
02397          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
02398          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
02399          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
02400          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
02401          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
02402          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
02403          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
02404          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
02405          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
02406          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
02407          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
02408          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
02409          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
02410          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
02411          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
02412        }
02413        ++pos;
02414        l_i = l_i2;
02415      }
02416      int numpos = pos;
02417 
02418      for ( pos = 0; pos < numpos; ++pos ) {
02419        double tmp;
02420        xscFile >> tmp;
02421        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02422        if ( pos == a_x ) cellBasisVector1.x = tmp;
02423        if ( pos == a_y ) cellBasisVector1.y = tmp;
02424        if ( pos == a_z ) cellBasisVector1.z = tmp;
02425        if ( pos == b_x ) cellBasisVector2.x = tmp;
02426        if ( pos == b_y ) cellBasisVector2.y = tmp;
02427        if ( pos == b_z ) cellBasisVector2.z = tmp;
02428        if ( pos == c_x ) cellBasisVector3.x = tmp;
02429        if ( pos == c_y ) cellBasisVector3.y = tmp;
02430        if ( pos == c_z ) cellBasisVector3.z = tmp;
02431        if ( pos == o_x ) cellOrigin.x = tmp;
02432        if ( pos == o_y ) cellOrigin.y = tmp;
02433        if ( pos == o_z ) cellOrigin.z = tmp;
02434        if ( pos == s_u ) strainRate2.x = tmp;
02435        if ( pos == s_v ) strainRate2.y = tmp;
02436        if ( pos == s_w ) strainRate2.z = tmp;
02437        if ( pos == s_x ) strainRate.x = tmp;
02438        if ( pos == s_y ) strainRate.y = tmp;
02439        if ( pos == s_z ) strainRate.z = tmp;
02440      }
02441 
02442    if ( latptr ) {
02443      Lattice test;
02444      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02445     
02446      if ( test.a_p() && ! lattice.a_p() ) {
02447        NAMD_die("cellBasisVector1 added during atom reinitialization");
02448      }
02449      if ( lattice.a_p() && ! test.a_p() ) {
02450        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
02451      }
02452      if ( test.b_p() && ! lattice.b_p() ) {
02453        NAMD_die("cellBasisVector2 added during atom reinitialization");
02454      }
02455      if ( lattice.b_p() && ! test.b_p() ) {
02456        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
02457      }
02458      if ( test.c_p() && ! lattice.c_p() ) {
02459        NAMD_die("cellBasisVector3 added during atom reinitialization");
02460      }
02461      if ( lattice.c_p() && ! test.c_p() ) {
02462        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
02463      }
02464 
02465      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02466    }
02467 
02468 }

void SimParameters::receive_SimParameters ( MIStream  ) 

Definition at line 7097 of file SimParameters.C.

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

07099 {
07100   msg->get(sizeof(SimParameters),(char*)this);
07101   if ( FFTWWisdomString ) {
07102     int fftwlen;
07103     msg->get(fftwlen);
07104     FFTWWisdomString = new char[fftwlen];
07105     msg->get(fftwlen,FFTWWisdomString);
07106 #ifdef NAMD_FFTW
07107 #ifdef NAMD_FFTW_3
07108     fftwf_import_wisdom_from_string(FFTWWisdomString);
07109 #else
07110     fftw_import_wisdom_from_string(FFTWWisdomString);
07111 #endif
07112 #endif
07113   }
07114   if ( tclBCScript ) {
07115     int tcllen;
07116     msg->get(tcllen);
07117     tclBCScript = new char[tcllen];
07118     msg->get(tcllen,tclBCScript);
07119   }
07120 
07121 #ifdef MEM_OPT_VERSION
07122   int filelen;
07123   msg->get(filelen);
07124   binAtomFile = new char[filelen];
07125   msg->get(filelen, binAtomFile);
07126   
07127   msg->get(filelen);
07128   binCoorFile = new char[filelen];
07129   msg->get(filelen, binCoorFile);
07130 
07131   if(binVelFile) {    
07132     msg->get(filelen);
07133     binVelFile = new char[filelen];
07134     msg->get(filelen, binVelFile);
07135   }
07136 
07137   if(binRefFile) {    
07138     msg->get(filelen);
07139     binRefFile = new char[filelen];
07140     msg->get(filelen, binRefFile);
07141   }
07142 #endif
07143 
07144 
07145   // The simParameters bit copy above put illegal values in the list pointers
07146   // So this resets everything so that unpacking will work.
07147   mgridforcelist.clear();
07148   mgridforcelist.unpack_data(msg);
07149   
07150   delete msg;
07151 }

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

Definition at line 169 of file SimParameters.C.

References accelMDalpha, accelMDE, accelMDGRestartFile, accelMDGSigma0D, accelMDGSigma0P, accelMDTalpha, accelMDTE, alchDispLambda, alchElecLambda, alchEquilSteps, alchFepElecOn, alchFepOn, alchFepOnAtStartup, alchFepWCADispOn, alchFepWCArcut1, alchFepWCArcut2, alchFepWCArcut3, alchFepWCARepuOn, alchIDWSfreq, alchLambda, alchLambda2, alchLambdaFreq, alchLambdaIDWS, alchOn, alchOnAtStartup, alchOutFreq, alchRepLambda, alchThermIntOn, alchThermIntOnAtStartup, atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, close_dcdfile(), close_veldcdfile(), commOnly, consForceScaling, constraintScaling, dcdFilename, dcdFrequency, drudeBondConst, drudeBondLen, drudeHardWallOn, eField, eFieldFreq, eFieldPhase, firstTimestep, fixCellDims, fixCellDimX, fixCellDimY, fixCellDimZ, fixedAtomsForces, fixedAtomsOn, fullElectFrequency, ComputeCUDAMgr::getComputeCUDAMgr(), initialTemp, langevin_useBAOAB, langevinOn, langevinOnAtStartup, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, maximumMove, minimizeOn, N, NAMD_die(), nonbondedFrequency, nonbondedScaling, outputEnergies, outputFilename, PMEOn, PRESSUREFACTOR, reassignTemp, rescaleTemp, restartFilename, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_MOD_FLOAT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, scriptArg1, scriptArg2, scriptArg3, scriptArg4, scriptArg5, scriptIntArg1, scriptIntArg2, scriptStringArg1, scriptStringArg2, ComputePmeUtil::select(), ComputeNonbondedUtil::select(), soluteScalingFactor, soluteScalingFactorCharge, soluteScalingFactorVdw, stirAxis, stirPivot, stochRescaleOn, stochRescaleTemp, surfaceTensionTarget, tclBCArgs, ComputeCUDAMgr::update(), useConstantArea, useConstantRatio, useFlexibleCell, useGroupPressure, and velDcdFilename.

Referenced by Node::scriptParam().

00169                                                                   {
00170 
00171   if ( CkMyRank() ) return;
00172 
00173 #define MAX_SCRIPT_PARAM_SIZE 128
00174 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00175 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00176 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00177 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
00178 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00179 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00180 
00181   SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00182   SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00183   SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00184   SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00185   SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00186   SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1)
00187   SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2)
00188   SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1)
00189   SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2)
00190   SCRIPT_PARSE_INT("numsteps",N)
00191   if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) {
00192     N = firstTimestep = atoi(value); return;
00193   }
00194   SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00195   SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00196   SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
00197   SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
00198   // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00199   if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) {
00200     langevinOn = atobool(value);
00201     if ( langevinOn && ! langevinOnAtStartup ) {
00202       NAMD_die("Langevin must be enabled at startup to disable and re-enable in script.");
00203     }
00204     return;
00205   }
00206   SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00207   SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
00208   SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
00209   SCRIPT_PARSE_BOOL("stochRescale",stochRescaleOn)
00210   SCRIPT_PARSE_FLOAT("stochRescaleTemp",stochRescaleTemp)
00211   SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00212   SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00213   SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00214   SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00215   SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
00216   SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
00217   SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
00218   SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
00219   SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00220   SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00221   SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
00222                         langevinPistonTarget,/PRESSUREFACTOR)
00223   SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00224   SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00225   SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00226   SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
00227                         surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
00228   SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00229   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
00230                         berendsenPressureTarget,/PRESSUREFACTOR)
00231   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
00232                         berendsenPressureCompressibility,*PRESSUREFACTOR)
00233   SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00234                                 berendsenPressureRelaxationTime)
00235   SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00236   SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00237   SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn)
00238   SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst)
00239   SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen)
00240   SCRIPT_PARSE_STRING("outputname",outputFilename)
00241   SCRIPT_PARSE_INT("outputEnergies",outputEnergies)
00242   SCRIPT_PARSE_STRING("restartname",restartFilename)
00243   SCRIPT_PARSE_INT("DCDfreq",dcdFrequency)
00244   if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
00245     close_dcdfile();  // *** implemented in Output.C ***
00246     strcpy(dcdFilename,value);
00247     return;
00248   }
00249   if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
00250     close_veldcdfile();  // *** implemented in Output.C ***
00251     strcpy(velDcdFilename,value);
00252     return;
00253   }
00254   SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00255   SCRIPT_PARSE_VECTOR("eField",eField)
00256   SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00257   SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
00258   SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 
00259   SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 
00260   SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 
00261   SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 
00262   SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 
00263   SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 
00264   SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile)
00265   SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00266   SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00267   if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
00268     NAMD_die("Can't yet modify mgridforcescale in a script");
00269     return;
00270   }
00271   if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
00272     NAMD_die("Can't yet modify mgridforcevoff in a script");
00273     return;
00274   }
00275    
00276   if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00277     if ( ! fixedAtomsOn )
00278       NAMD_die("FixedAtoms may not be enabled in a script.");
00279     if ( ! fixedAtomsForces )
00280       NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00281     fixedAtomsOn = atobool(value);
00282     return;
00283   }
00284 
00285 //fepb
00286   if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) {
00287     alchOn = atobool(value);
00288     if ( alchOn && ! alchOnAtStartup ) {
00289        NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script.");
00290     }
00291     alchFepOn = alchOn && alchFepOnAtStartup;
00292     alchThermIntOn = alchOn && alchThermIntOnAtStartup;
00293     ComputeNonbondedUtil::select();
00294     if ( PMEOn ) ComputePmeUtil::select();
00295     return;
00296   }
00297   SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
00298 
00299   if ( ! strncasecmp(param,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00300     alchRepLambda = atof(value);
00301     alchFepWCARepuOn = true;
00302     alchFepWCADispOn = false;
00303     alchFepElecOn    = false;
00304     ComputeNonbondedUtil::select();
00305     return;
00306   }
00307 
00308   if ( ! strncasecmp(param,"alchDispLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00309     alchDispLambda = atof(value);
00310     alchFepWCARepuOn = false;
00311     alchFepWCADispOn = true;
00312     alchFepElecOn    = false;
00313     ComputeNonbondedUtil::select();
00314     return;
00315   }
00316 
00317   if ( ! strncasecmp(param,"alchElecLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00318     alchElecLambda = atof(value);
00319     alchFepWCARepuOn = false;
00320     alchFepWCADispOn = false;
00321     alchFepElecOn    = true;
00322     ComputeNonbondedUtil::select();
00323     return;
00324   }
00325 
00326 
00327   if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) {
00328     alchFepWCArcut1 = atof(value);
00329     ComputeNonbondedUtil::select();
00330     return;
00331   }
00332 
00333   if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) {
00334     alchFepWCArcut2 = atof(value);
00335     ComputeNonbondedUtil::select();
00336     return;
00337   }
00338 
00339   if ( ! strncasecmp(param,"alchFepWCArcut3",MAX_SCRIPT_PARAM_SIZE) ) {
00340     alchFepWCArcut3 = atof(value);
00341     ComputeNonbondedUtil::select();
00342     return;
00343   }
00344 
00345   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00346     alchLambda = atof(value);
00347     if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
00348       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00349     }
00350     ComputeNonbondedUtil::select();
00351     return;
00352   }
00353 
00354   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00355     alchLambda2 = atof(value);
00356     if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
00357       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00358     }
00359     ComputeNonbondedUtil::select();
00360     return;
00361   }
00362 
00363   if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
00364     alchLambdaIDWS = atof(value);
00365     if ( alchLambdaIDWS > 1. ) {
00366       NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
00367     }
00368     // Switch lambda2 every other cycle of fullElectFrequency steps
00369     // or every other nonbondedFrequency steps if undefined
00370     // or every alchOutFreq steps if larger (no need to switch faster that we output)
00371     alchIDWSfreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency;
00372     if ( alchOutFreq > alchIDWSfreq )
00373       alchIDWSfreq = alchOutFreq;
00374     ComputeNonbondedUtil::select();
00375     return;
00376   }
00377 
00378   if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
00379     alchLambdaFreq = atoi(value);
00380     if ( alchLambdaIDWS >= 0 ) {
00381       NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n");
00382     }
00383     ComputeNonbondedUtil::select();
00384     return;
00385   }
00386 //fepe
00387 
00388   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00389     nonbondedScaling = atof(value);
00390     ComputeNonbondedUtil::select();
00391     return;
00392   }
00393 
00394   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00395     commOnly = atobool(value);
00396     ComputeNonbondedUtil::select();
00397     return;
00398   }
00399 
00400   // REST2 - We don't have to make any changes to ComputeNonbondedUtil
00401   // other than recalculating the LJTable.  Skip doing the other stuff.
00402   if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) {
00403     soluteScalingFactor = atof(value);
00404     if (soluteScalingFactor < 0.0) {
00405       NAMD_die("Solute scaling factor should be non-negative\n");
00406     }
00407     soluteScalingFactorCharge = soluteScalingFactor;
00408     soluteScalingFactorVdw = soluteScalingFactor;
00409     // update LJTable for CPU
00410     ComputeNonbondedUtil::select();
00411 #ifdef NAMD_CUDA
00412     // update LJTable for GPU, needs CPU update first
00413     ComputeCUDAMgr::getComputeCUDAMgr()->update();
00414 #endif
00415     return;
00416   }
00417   if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) {
00418     soluteScalingFactorVdw = atof(value);
00419     if (soluteScalingFactorVdw < 0.0) {
00420       NAMD_die("Solute scaling factor for van der Waals "
00421           "should be non-negative\n");
00422     }
00423     // update LJTable for CPU
00424     ComputeNonbondedUtil::select();
00425 #ifdef NAMD_CUDA
00426     // update LJTable for GPU, needs CPU update first
00427     ComputeCUDAMgr::getComputeCUDAMgr()->update();
00428 #endif
00429     return;
00430   }
00431   if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) {
00432     soluteScalingFactorCharge = atof(value);
00433     if (soluteScalingFactorCharge < 0.0) {
00434       NAMD_die("Solute scaling factor for electrostatics "
00435           "should be non-negative\n");
00436     }
00437     return;
00438   }
00439 
00440   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00441   sprintf(error,"Setting parameter %s from script failed!\n",param);
00442   NAMD_die(error);
00443 
00444 }

void SimParameters::send_SimParameters ( MOStream  ) 

Definition at line 7039 of file SimParameters.C.

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

07041 {
07042   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
07043   if ( msg == NULL )
07044   {
07045     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
07046   }*/
07047 
07048   msg->put(sizeof(SimParameters),(char*)this);
07049   if ( FFTWWisdomString ) {
07050     int fftwlen = strlen(FFTWWisdomString) + 1;
07051     msg->put(fftwlen);
07052     msg->put(fftwlen,FFTWWisdomString);
07053   }
07054   if ( tclBCScript ) {
07055     int tcllen = strlen(tclBCScript) + 1;
07056     msg->put(tcllen);
07057     msg->put(tcllen,tclBCScript);
07058   }
07059 
07060 #ifdef MEM_OPT_VERSION
07061   int filelen = strlen(binAtomFile)+1;
07062   msg->put(filelen);
07063   msg->put(filelen, binAtomFile);
07064 
07065   filelen = strlen(binCoorFile)+1;
07066   msg->put(filelen);
07067   msg->put(filelen, binCoorFile);
07068 
07069   if(binVelFile) {
07070     filelen = strlen(binVelFile)+1;
07071     msg->put(filelen);
07072     msg->put(filelen, binVelFile);
07073   }
07074 
07075   if(binRefFile) {
07076     filelen = strlen(binRefFile)+1;
07077     msg->put(filelen);
07078     msg->put(filelen, binRefFile);
07079   }
07080 #endif
07081 
07082   mgridforcelist.pack_data(msg);
07083   
07084   msg->end();
07085 }


Member Data Documentation

int SimParameters::aaAngleExp

Definition at line 954 of file SimParameters.h.

BigReal SimParameters::accelMDalpha

Definition at line 609 of file SimParameters.h.

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

Bool SimParameters::accelMDDebugOn

Definition at line 604 of file SimParameters.h.

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

Bool SimParameters::accelMDdihe

Definition at line 602 of file SimParameters.h.

Referenced by ComputeHomeTuples< AnisoElem, aniso, aniso >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().

Bool SimParameters::accelMDdual

Definition at line 603 of file SimParameters.h.

Referenced by ComputeHomeTuples< AnisoElem, aniso, aniso >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().

BigReal SimParameters::accelMDE

Definition at line 608 of file SimParameters.h.

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

BigReal SimParameters::accelMDFirstStep

Definition at line 605 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDG

Definition at line 613 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDPrepSteps

Definition at line 617 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDSteps

Definition at line 615 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiPrepSteps

Definition at line 618 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiSteps

Definition at line 616 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGiE

Definition at line 614 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGresetVaftercmd

Definition at line 623 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGRestart

Definition at line 621 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

char SimParameters::accelMDGRestartFile[128]

Definition at line 622 of file SimParameters.h.

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

BigReal SimParameters::accelMDGSigma0D

Definition at line 620 of file SimParameters.h.

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

BigReal SimParameters::accelMDGSigma0P

Definition at line 619 of file SimParameters.h.

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

BigReal SimParameters::accelMDLastStep

Definition at line 606 of file SimParameters.h.

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

Bool SimParameters::accelMDOn

Definition at line 601 of file SimParameters.h.

Referenced by Controller::calcPressure(), ComputeHomeTuples< AnisoElem, aniso, aniso >::ComputeHomeTuples(), Controller::Controller(), Sequencer::integrate(), Controller::receivePressure(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and Sequencer::Sequencer().

int SimParameters::accelMDOutFreq

Definition at line 607 of file SimParameters.h.

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

BigReal SimParameters::accelMDTalpha

Definition at line 611 of file SimParameters.h.

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

BigReal SimParameters::accelMDTE

Definition at line 610 of file SimParameters.h.

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

BigReal SimParameters::adaptTempAutoDt

Definition at line 634 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempBins

Definition at line 635 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempCgamma

Definition at line 637 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempDebug

Definition at line 627 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

BigReal SimParameters::adaptTempDt

Definition at line 636 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempFirstStep

Definition at line 628 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

int SimParameters::adaptTempFreq

Definition at line 631 of file SimParameters.h.

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

char SimParameters::adaptTempInFile[128]

Definition at line 640 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempLangevin

Definition at line 638 of file SimParameters.h.

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

int SimParameters::adaptTempLastStep

Definition at line 629 of file SimParameters.h.

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

Bool SimParameters::adaptTempOn

Definition at line 626 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 630 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRandom

Definition at line 643 of file SimParameters.h.

Bool SimParameters::adaptTempRescale

Definition at line 639 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

char SimParameters::adaptTempRestartFile[128]

Definition at line 641 of file SimParameters.h.

int SimParameters::adaptTempRestartFreq

Definition at line 642 of file SimParameters.h.

Referenced by Controller::adaptTempWriteRestart().

BigReal SimParameters::adaptTempTmax

Definition at line 633 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempTmin

Definition at line 632 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::alchBondDecouple

Definition at line 425 of file SimParameters.h.

BigReal SimParameters::alchBondLambdaEnd

Definition at line 419 of file SimParameters.h.

Bool SimParameters::alchDecouple

Definition at line 424 of file SimParameters.h.

BigReal SimParameters::alchDispLambda

Definition at line 396 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambda

Definition at line 397 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambdaStart

Definition at line 408 of file SimParameters.h.

Bool SimParameters::alchEnsembleAvg

Definition at line 403 of file SimParameters.h.

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

int SimParameters::alchEquilSteps

Definition at line 405 of file SimParameters.h.

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

Bool SimParameters::alchFepElecOn

Definition at line 383 of file SimParameters.h.

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

Bool SimParameters::alchFepOn

Definition at line 379 of file SimParameters.h.

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

Bool SimParameters::alchFepOnAtStartup

Definition at line 376 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::alchFepWCADispOn

Definition at line 382 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut1

Definition at line 398 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut2

Definition at line 399 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut3

Definition at line 400 of file SimParameters.h.

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

Bool SimParameters::alchFepWCARepuOn

Definition at line 381 of file SimParameters.h.

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

Bool SimParameters::alchFepWhamOn

Definition at line 384 of file SimParameters.h.

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

int SimParameters::alchIDWSfreq

Definition at line 389 of file SimParameters.h.

Referenced by getCurrentLambda2(), Controller::outputFepEnergy(), scriptSet(), and Controller::writeFepEnergyData().

BigReal SimParameters::alchLambda

Definition at line 386 of file SimParameters.h.

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

BigReal SimParameters::alchLambda2

Definition at line 387 of file SimParameters.h.

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

int SimParameters::alchLambdaFreq

Definition at line 390 of file SimParameters.h.

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

BigReal SimParameters::alchLambdaIDWS

Definition at line 388 of file SimParameters.h.

Referenced by getCurrentLambda2(), Controller::outputFepEnergy(), Controller::printFepMessage(), scriptSet(), and Controller::writeFepEnergyData().

int SimParameters::alchMethod

Definition at line 385 of file SimParameters.h.

Bool SimParameters::alchOn

Definition at line 378 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), NamdState::loadStructure(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), Molecule::receive_Molecule(), scriptSet(), and Molecule::send_Molecule().

Bool SimParameters::alchOnAtStartup

Definition at line 375 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::alchOutFile[128]

Definition at line 404 of file SimParameters.h.

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

int SimParameters::alchOutFreq

Definition at line 402 of file SimParameters.h.

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

BigReal SimParameters::alchRepLambda

Definition at line 395 of file SimParameters.h.

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

BigReal SimParameters::alchTemp

Definition at line 401 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOn

Definition at line 380 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOnAtStartup

Definition at line 377 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 414 of file SimParameters.h.

Referenced by Controller::printEnergies().

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 406 of file SimParameters.h.

BigReal SimParameters::alpha_cutoff

Definition at line 519 of file SimParameters.h.

BigReal SimParameters::alpha_max

Definition at line 520 of file SimParameters.h.

Bool SimParameters::amberOn

Definition at line 975 of file SimParameters.h.

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

char SimParameters::auxFilename[128]

Definition at line 200 of file SimParameters.h.

Referenced by CollectionMaster::receiveDataStream().

Bool SimParameters::benchTimestep

Definition at line 156 of file SimParameters.h.

BigReal SimParameters::berendsenPressureCompressibility

Definition at line 667 of file SimParameters.h.

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

int SimParameters::berendsenPressureFreq

Definition at line 669 of file SimParameters.h.

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

Bool SimParameters::berendsenPressureOn

Definition at line 665 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 668 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureTarget

Definition at line 666 of file SimParameters.h.

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

Bool SimParameters::binaryOutput

Definition at line 217 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Bool SimParameters::binaryRestart

Definition at line 215 of file SimParameters.h.

char* SimParameters::binAtomFile

Definition at line 1013 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binCoorFile

Definition at line 1014 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binRefFile

Definition at line 1016 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binVelFile

Definition at line 1015 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

int SimParameters::bondedCUDA

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

Definition at line 787 of file SimParameters.h.

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

zVector SimParameters::cellBasisVector1

Definition at line 116 of file SimParameters.h.

Referenced by readExtendedSystem().

zVector SimParameters::cellBasisVector2

Definition at line 117 of file SimParameters.h.

Referenced by readExtendedSystem().

zVector SimParameters::cellBasisVector3

Definition at line 118 of file SimParameters.h.

Referenced by readExtendedSystem().

zVector SimParameters::cellOrigin

Definition at line 119 of file SimParameters.h.

Referenced by readExtendedSystem().

Bool SimParameters::COLDOn

Definition at line 573 of file SimParameters.h.

BigReal SimParameters::COLDRate

Definition at line 575 of file SimParameters.h.

BigReal SimParameters::COLDTemp

Definition at line 576 of file SimParameters.h.

Bool SimParameters::colvarsOn

Definition at line 550 of file SimParameters.h.

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

Bool SimParameters::commOnly

Definition at line 914 of file SimParameters.h.

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

Bool SimParameters::comMove

Definition at line 178 of file SimParameters.h.

Referenced by ParallelIOMgr::bcastMolInfo(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), Controller::receivePressure(), ParallelIOMgr::recvMolInfo(), and ParallelIOMgr::updateMolInfo().

char SimParameters::computeMapFilename[128]

Definition at line 1022 of file SimParameters.h.

char SimParameters::consForceFile[128]

Definition at line 866 of file SimParameters.h.

Bool SimParameters::consForceOn

Definition at line 865 of file SimParameters.h.

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

BigReal SimParameters::consForceScaling

Definition at line 867 of file SimParameters.h.

Referenced by ComputeConsForce::doForce(), and scriptSet().

char SimParameters::consTorqueAxisFile[128]

Definition at line 331 of file SimParameters.h.

char SimParameters::consTorqueFile[128]

Definition at line 329 of file SimParameters.h.

BigReal SimParameters::consTorqueGlobVal

Definition at line 333 of file SimParameters.h.

Bool SimParameters::consTorqueOn

Definition at line 328 of file SimParameters.h.

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

char SimParameters::consTorquePivotFile[128]

Definition at line 332 of file SimParameters.h.

char SimParameters::consTorqueValFile[128]

Definition at line 334 of file SimParameters.h.

int SimParameters::constraintExp

Definition at line 252 of file SimParameters.h.

BigReal SimParameters::constraintScaling

Definition at line 280 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::constraintsOn

Definition at line 250 of file SimParameters.h.

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

Bool SimParameters::constrXOn

Definition at line 271 of file SimParameters.h.

Bool SimParameters::constrYOn

Definition at line 271 of file SimParameters.h.

Bool SimParameters::constrZOn

Definition at line 271 of file SimParameters.h.

Bool SimParameters::cosAngles

Definition at line 539 of file SimParameters.h.

BigReal SimParameters::coulomb_radius_offset

Definition at line 513 of file SimParameters.h.

BigReal SimParameters::cutoff

Definition at line 219 of file SimParameters.h.

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

char SimParameters::cylindricalBCAxis

Definition at line 838 of file SimParameters.h.

int SimParameters::cylindricalBCexp1

Definition at line 843 of file SimParameters.h.

int SimParameters::cylindricalBCexp2

Definition at line 844 of file SimParameters.h.

BigReal SimParameters::cylindricalBCk1

Definition at line 845 of file SimParameters.h.

BigReal SimParameters::cylindricalBCk2

Definition at line 846 of file SimParameters.h.

BigReal SimParameters::cylindricalBCl1

Definition at line 841 of file SimParameters.h.

BigReal SimParameters::cylindricalBCl2

Definition at line 842 of file SimParameters.h.

Bool SimParameters::cylindricalBCOn

Definition at line 835 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::cylindricalBCr1

Definition at line 839 of file SimParameters.h.

BigReal SimParameters::cylindricalBCr2

Definition at line 840 of file SimParameters.h.

zVector SimParameters::cylindricalCenter

Definition at line 837 of file SimParameters.h.

BigReal SimParameters::daCutoffDist

Definition at line 961 of file SimParameters.h.

BigReal SimParameters::daOffDist

Definition at line 961 of file SimParameters.h.

BigReal SimParameters::daOnDist

Definition at line 961 of file SimParameters.h.

char SimParameters::dcdFilename[128]

Definition at line 201 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::dcdFrequency

Definition at line 191 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::dcdUnitCell

Definition at line 193 of file SimParameters.h.

BigReal SimParameters::dhaCutoffAngle

Definition at line 957 of file SimParameters.h.

BigReal SimParameters::dhaOffAngle

Definition at line 957 of file SimParameters.h.

BigReal SimParameters::dhaOnAngle

Definition at line 957 of file SimParameters.h.

BigReal SimParameters::dielectric

Definition at line 185 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::dihedralOn

Definition at line 572 of file SimParameters.h.

Bool SimParameters::disableTopology

Definition at line 153 of file SimParameters.h.

int SimParameters::distAttExp

Definition at line 954 of file SimParameters.h.

int SimParameters::distRepExp

Definition at line 954 of file SimParameters.h.

BigReal SimParameters::drudeBondConst

Definition at line 531 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::drudeBondLen

Definition at line 529 of file SimParameters.h.

Referenced by scriptSet(), and Sequencer::submitMinimizeReductions().

BigReal SimParameters::drudeDamping

Definition at line 527 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::drudeHardWallOn

Definition at line 525 of file SimParameters.h.

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

BigReal SimParameters::drudeNbtholeCut

Definition at line 532 of file SimParameters.h.

Bool SimParameters::drudeOn

Definition at line 524 of file SimParameters.h.

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

BigReal SimParameters::drudeTemp

Definition at line 526 of file SimParameters.h.

Referenced by Sequencer::langevinVelocitiesBBK2().

BigReal SimParameters::dt

Definition at line 112 of file SimParameters.h.

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

zVector SimParameters::eField

Definition at line 850 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::eFieldFreq

Definition at line 851 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::eFieldNormalized

Definition at line 849 of file SimParameters.h.

Bool SimParameters::eFieldOn

Definition at line 848 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::eFieldPhase

Definition at line 852 of file SimParameters.h.

Referenced by scriptSet().

ExclusionSettings SimParameters::exclude

Definition at line 186 of file SimParameters.h.

Referenced by buildExclusions().

Bool SimParameters::excludeFromPressure

Definition at line 654 of file SimParameters.h.

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

char SimParameters::extCoordFilename[128]

Definition at line 450 of file SimParameters.h.

char SimParameters::extForceFilename[128]

Definition at line 451 of file SimParameters.h.

char SimParameters::extForcesCommand[256]

Definition at line 449 of file SimParameters.h.

Bool SimParameters::extForcesOn

Definition at line 448 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::extraBondsOn

Definition at line 863 of file SimParameters.h.

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

Bool SimParameters::FFTWEstimate

Definition at line 804 of file SimParameters.h.

Bool SimParameters::FFTWPatient

Definition at line 805 of file SimParameters.h.

Bool SimParameters::FFTWUseWisdom

Definition at line 806 of file SimParameters.h.

char SimParameters::FFTWWisdomFile[128]

Definition at line 807 of file SimParameters.h.

char* SimParameters::FFTWWisdomString

Definition at line 808 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

int SimParameters::firstLdbStep

Definition at line 130 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::firstTimestep

Definition at line 886 of file SimParameters.h.

Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::algorithm(), colvarproxy_namd::colvarproxy_namd(), getCurrentLambda(), getLambdaDelta(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), Sequencer::integrate(), Controller::integrate(), Sequencer::minimize(), Controller::minimize(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiming(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Controller::rescaleaccelMD(), scriptSet(), and Controller::writeFepEnergyData().

Bool SimParameters::fixCellDims

Definition at line 660 of file SimParameters.h.

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

Bool SimParameters::fixCellDimX

Definition at line 661 of file SimParameters.h.

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

Bool SimParameters::fixCellDimY

Definition at line 662 of file SimParameters.h.

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

Bool SimParameters::fixCellDimZ

Definition at line 663 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsForceOutput

Definition at line 554 of file SimParameters.h.

Bool SimParameters::fixedAtomsForces

Definition at line 553 of file SimParameters.h.

Referenced by ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples(), scriptSet(), and ParallelIOMgr::updateMolInfo().

Bool SimParameters::fixedAtomsOn

Definition at line 552 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), ParallelIOMgr::bcastHydroBasedCounter(), Sequencer::berendsenPressure(), ParallelIOMgr::calcAtomsInEachPatch(), Sequencer::calcFixVirial(), Sequencer::correctMomentum(), Sequencer::langevinPiston(), NamdState::loadStructure(), ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples(), Sequencer::minimizeMoveDownhill(), Sequencer::multigratorPressure(), Sequencer::newMinimizeDirection(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Controller::receivePressure(), ParallelIOMgr::recvAtomsCntPerPatch(), Sequencer::reinitVelocities(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), scriptSet(), Molecule::send_Molecule(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().

int SimParameters::FMAFFTBlock

Definition at line 707 of file SimParameters.h.

Bool SimParameters::FMAFFTOn

Definition at line 706 of file SimParameters.h.

int SimParameters::FMALevels

Definition at line 704 of file SimParameters.h.

int SimParameters::FMAMp

Definition at line 705 of file SimParameters.h.

Bool SimParameters::FMAOn

Definition at line 703 of file SimParameters.h.

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

BigReal SimParameters::fmaTheta

Definition at line 126 of file SimParameters.h.

int SimParameters::FMMLevels

Definition at line 751 of file SimParameters.h.

Bool SimParameters::FMMOn

Definition at line 750 of file SimParameters.h.

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

BigReal SimParameters::FMMPadding

Definition at line 752 of file SimParameters.h.

char SimParameters::forceDcdFilename[128]

Definition at line 203 of file SimParameters.h.

int SimParameters::forceDcdFrequency

Definition at line 196 of file SimParameters.h.

Bool SimParameters::freeEnergyOn

Definition at line 548 of file SimParameters.h.

Referenced by ParallelIOMgr::freeMolSpace().

BigReal SimParameters::fsMax

Definition at line 510 of file SimParameters.h.

Bool SimParameters::fullDirectOn

Definition at line 709 of file SimParameters.h.

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

int SimParameters::fullElectFrequency

Definition at line 124 of file SimParameters.h.

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

BigReal SimParameters::gbis_beta

Definition at line 517 of file SimParameters.h.

BigReal SimParameters::gbis_delta

Definition at line 516 of file SimParameters.h.

BigReal SimParameters::gbis_gamma

Definition at line 518 of file SimParameters.h.

Bool SimParameters::GBISOn

Definition at line 509 of file SimParameters.h.

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

Bool SimParameters::GBISserOn

Definition at line 511 of file SimParameters.h.

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

Bool SimParameters::genCompressedPsf

Definition at line 997 of file SimParameters.h.

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

Bool SimParameters::globalForcesOn

Definition at line 540 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::globalOn

Definition at line 571 of file SimParameters.h.

char SimParameters::goCoordinates[128]

Definition at line 291 of file SimParameters.h.

Bool SimParameters::goForcesOn

Definition at line 289 of file SimParameters.h.

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

Bool SimParameters::goGroPair

Definition at line 288 of file SimParameters.h.

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

GoChoices SimParameters::goMethod

Definition at line 293 of file SimParameters.h.

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

char SimParameters::goParameters[128]

Definition at line 290 of file SimParameters.h.

Bool SimParameters::gridforcechecksize

Definition at line 263 of file SimParameters.h.

Bool SimParameters::gridforceContA1

Definition at line 258 of file SimParameters.h.

Bool SimParameters::gridforceContA2

Definition at line 259 of file SimParameters.h.

Bool SimParameters::gridforceContA3

Definition at line 260 of file SimParameters.h.

Bool SimParameters::gridforceLite

Definition at line 262 of file SimParameters.h.

Bool SimParameters::gridforceOn

Definition at line 255 of file SimParameters.h.

zVector SimParameters::gridforceScale

Definition at line 257 of file SimParameters.h.

zVector SimParameters::gridforceVOffset

Definition at line 261 of file SimParameters.h.

Bool SimParameters::gridforceVolts

Definition at line 256 of file SimParameters.h.

Bool SimParameters::gromacsOn

Definition at line 980 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::haAngleExp

Definition at line 954 of file SimParameters.h.

BigReal SimParameters::hgroupCutoff

Definition at line 898 of file SimParameters.h.

int SimParameters::hybridGroupSize

Definition at line 134 of file SimParameters.h.

Bool SimParameters::HydrogenBonds

Definition at line 944 of file SimParameters.h.

Bool SimParameters::ignoreMass

Definition at line 895 of file SimParameters.h.

int SimParameters::IMDfreq

Definition at line 966 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::IMDignore

Definition at line 969 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDignoreForces

Definition at line 971 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDon

Definition at line 964 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::IMDport

Definition at line 965 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDwait

Definition at line 967 of file SimParameters.h.

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

BigReal SimParameters::initialTemp

Definition at line 176 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 515 of file SimParameters.h.

BigReal SimParameters::kappa

Definition at line 514 of file SimParameters.h.

Bool SimParameters::langevin_useBAOAB

Definition at line 561 of file SimParameters.h.

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

BigReal SimParameters::langevinDamping

Definition at line 559 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinHydrogen

Definition at line 560 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinOn

Definition at line 557 of file SimParameters.h.

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

Bool SimParameters::langevinOnAtStartup

Definition at line 556 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::langevinPistonBarrier

Definition at line 672 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

BigReal SimParameters::langevinPistonDecay

Definition at line 675 of file SimParameters.h.

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

Bool SimParameters::langevinPistonOn

Definition at line 671 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonPeriod

Definition at line 674 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTarget

Definition at line 673 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTemp

Definition at line 676 of file SimParameters.h.

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

BigReal SimParameters::langevinTemp

Definition at line 558 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.

Lattice SimParameters::lattice

Definition at line 120 of file SimParameters.h.

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

Bool SimParameters::LCPOOn

Definition at line 521 of file SimParameters.h.

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

int SimParameters::ldBalancer

Definition at line 127 of file SimParameters.h.

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.

BigReal SimParameters::ldbPMEBackgroundScaling

Definition at line 136 of file SimParameters.h.

BigReal SimParameters::ldbRelativeGrainsize

Definition at line 138 of file SimParameters.h.

int SimParameters::ldbStrategy

Definition at line 128 of file SimParameters.h.

Bool SimParameters::ldbUnloadOne

Definition at line 170 of file SimParameters.h.

Bool SimParameters::ldbUnloadOutputPEs

Definition at line 171 of file SimParameters.h.

Bool SimParameters::ldbUnloadPME

Definition at line 168 of file SimParameters.h.

Bool SimParameters::ldbUnloadZero

Definition at line 169 of file SimParameters.h.

int SimParameters::lesFactor

Definition at line 430 of file SimParameters.h.

Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().

Bool SimParameters::lesOn

Definition at line 429 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples(), Sequencer::reassignVelocities(), Molecule::receive_Molecule(), Sequencer::reinitVelocities(), and Molecule::send_Molecule().

Bool SimParameters::lesReduceMass

Definition at line 432 of file SimParameters.h.

Bool SimParameters::lesReduceTemp

Definition at line 431 of file SimParameters.h.

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

BigReal SimParameters::limitDist

Definition at line 226 of file SimParameters.h.

Bool SimParameters::LJcorrection

Definition at line 111 of file SimParameters.h.

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

Bool SimParameters::loadComputeMap

Definition at line 1024 of file SimParameters.h.

Bool SimParameters::lonepairs

Definition at line 108 of file SimParameters.h.

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

int SimParameters::longSplitting

Definition at line 892 of file SimParameters.h.

BigReal SimParameters::loweAndersenCutoff

Definition at line 568 of file SimParameters.h.

Bool SimParameters::loweAndersenOn

Definition at line 565 of file SimParameters.h.

Referenced by Sequencer::integrate().

BigReal SimParameters::loweAndersenRate

Definition at line 567 of file SimParameters.h.

BigReal SimParameters::loweAndersenTemp

Definition at line 566 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::mallocTest

Definition at line 1001 of file SimParameters.h.

Referenced by Node::startup().

BigReal SimParameters::margin

Definition at line 220 of file SimParameters.h.

Bool SimParameters::martiniDielAllow

Definition at line 236 of file SimParameters.h.

Bool SimParameters::martiniSwitching

Definition at line 234 of file SimParameters.h.

int SimParameters::maxExclusionFlags

Definition at line 932 of file SimParameters.h.

BigReal SimParameters::maximumMove

Definition at line 820 of file SimParameters.h.

Referenced by Sequencer::maximumMove(), and scriptSet().

int SimParameters::maxPairPart

Definition at line 920 of file SimParameters.h.

int SimParameters::maxPatches

Definition at line 167 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::maxSelfPart

Definition at line 918 of file SimParameters.h.

Bool SimParameters::mergeCrossterms

Definition at line 884 of file SimParameters.h.

Referenced by Controller::printEnergies().

MGridforceParamsList SimParameters::mgridforcelist

Definition at line 266 of file SimParameters.h.

Referenced by Molecule::build_gridforce_params(), receive_SimParameters(), Node::reloadGridforceGrid(), send_SimParameters(), and Node::updateGridScale().

Bool SimParameters::mgridforceOn

Definition at line 265 of file SimParameters.h.

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

int SimParameters::mic_deviceThreshold

Definition at line 1032 of file SimParameters.h.

int SimParameters::mic_hostSplit

Definition at line 1027 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p1

Definition at line 1029 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p2

Definition at line 1030 of file SimParameters.h.

int SimParameters::mic_numParts_self_p1

Definition at line 1028 of file SimParameters.h.

int SimParameters::mic_singleKernel

Definition at line 1033 of file SimParameters.h.

int SimParameters::mic_unloadMICPEs

Definition at line 1031 of file SimParameters.h.

int SimParameters::minAtomsPerPatch

Definition at line 930 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

BigReal SimParameters::minBabyStep

Definition at line 817 of file SimParameters.h.

Bool SimParameters::minimizeCGOn

Definition at line 814 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::minimizeOn

Definition at line 819 of file SimParameters.h.

Referenced by Sequencer::minimizationQuenchVelocity(), and scriptSet().

BigReal SimParameters::minLineGoal

Definition at line 818 of file SimParameters.h.

Referenced by Controller::minimize().

BigReal SimParameters::minTinyStep

Definition at line 816 of file SimParameters.h.

Bool SimParameters::minVerbose

Definition at line 815 of file SimParameters.h.

Referenced by Controller::minimize().

Bool SimParameters::miscForcesOn

Definition at line 549 of file SimParameters.h.

int SimParameters::mollyIter

Definition at line 902 of file SimParameters.h.

int SimParameters::mollyOn

Definition at line 900 of file SimParameters.h.

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

BigReal SimParameters::mollyTol

Definition at line 901 of file SimParameters.h.

char SimParameters::movDragFile[128]

Definition at line 311 of file SimParameters.h.

BigReal SimParameters::movDragGlobVel

Definition at line 313 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

Bool SimParameters::movDragOn

Definition at line 310 of file SimParameters.h.

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

char SimParameters::movDragVelFile[128]

Definition at line 314 of file SimParameters.h.

Bool SimParameters::movingConstraintsOn

Definition at line 297 of file SimParameters.h.

zVector SimParameters::movingConsVel

Definition at line 299 of file SimParameters.h.

int SimParameters::MSMApprox

Definition at line 719 of file SimParameters.h.

int SimParameters::MSMBlockSizeX

Definition at line 729 of file SimParameters.h.

int SimParameters::MSMBlockSizeY

Definition at line 730 of file SimParameters.h.

int SimParameters::MSMBlockSizeZ

Definition at line 731 of file SimParameters.h.

BigReal SimParameters::MSMGridSpacing

Definition at line 733 of file SimParameters.h.

int SimParameters::MSMLevels

Definition at line 725 of file SimParameters.h.

Bool SimParameters::MSMOn

Definition at line 712 of file SimParameters.h.

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

BigReal SimParameters::MSMPadding

Definition at line 735 of file SimParameters.h.

int SimParameters::MSMQuality

Definition at line 715 of file SimParameters.h.

Bool SimParameters::MsmSerialOn

Definition at line 748 of file SimParameters.h.

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

int SimParameters::MSMSplit

Definition at line 722 of file SimParameters.h.

BigReal SimParameters::MSMxmax

Definition at line 742 of file SimParameters.h.

BigReal SimParameters::MSMxmin

Definition at line 741 of file SimParameters.h.

BigReal SimParameters::MSMymax

Definition at line 744 of file SimParameters.h.

BigReal SimParameters::MSMymin

Definition at line 743 of file SimParameters.h.

BigReal SimParameters::MSMzmax

Definition at line 746 of file SimParameters.h.

BigReal SimParameters::MSMzmin

Definition at line 745 of file SimParameters.h.

MTSChoices SimParameters::MTSAlgorithm

Definition at line 889 of file SimParameters.h.

Referenced by Sequencer::integrate().

int SimParameters::multigratorNoseHooverChainLength

Definition at line 685 of file SimParameters.h.

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

Bool SimParameters::multigratorOn

Definition at line 678 of file SimParameters.h.

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

int SimParameters::multigratorPressureFreq

Definition at line 681 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureRelaxationTime

Definition at line 680 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureTarget

Definition at line 679 of file SimParameters.h.

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

int SimParameters::multigratorTemperatureFreq

Definition at line 684 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureRelaxationTime

Definition at line 683 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureTarget

Definition at line 682 of file SimParameters.h.

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

int SimParameters::N

Definition at line 113 of file SimParameters.h.

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

int SimParameters::nonbondedFrequency

Definition at line 122 of file SimParameters.h.

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

BigReal SimParameters::nonbondedScaling

Definition at line 190 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg(), and scriptSet().

Bool SimParameters::noPatchesOnOne

Definition at line 174 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnOutputPEs

Definition at line 173 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnZero

Definition at line 172 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::numAtomsPair

Definition at line 926 of file SimParameters.h.

int SimParameters::numAtomsPair2

Definition at line 928 of file SimParameters.h.

int SimParameters::numAtomsSelf

Definition at line 922 of file SimParameters.h.

int SimParameters::numAtomsSelf2

Definition at line 924 of file SimParameters.h.

int SimParameters::numinputprocs

Definition at line 1012 of file SimParameters.h.

Referenced by ParallelIOMgr::initialize(), and NamdState::loadStructure().

int SimParameters::numoutputprocs

Definition at line 1019 of file SimParameters.h.

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

int SimParameters::numoutputwrts

Definition at line 1020 of file SimParameters.h.

Referenced by ParallelIOMgr::initialize(), and NamdState::loadStructure().

int SimParameters::numTraceSteps

Definition at line 141 of file SimParameters.h.

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

int SimParameters::outputCudaTiming

Definition at line 878 of file SimParameters.h.

int SimParameters::outputEnergies

Definition at line 869 of file SimParameters.h.

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

char SimParameters::outputFilename[128]

Definition at line 205 of file SimParameters.h.

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

Bool SimParameters::outputMaps

Definition at line 149 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

int SimParameters::outputMomenta

Definition at line 872 of file SimParameters.h.

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

int SimParameters::outputPairlists

Definition at line 248 of file SimParameters.h.

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

Bool SimParameters::outputPatchDetails

Definition at line 934 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

int SimParameters::outputPressure

Definition at line 881 of file SimParameters.h.

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

int SimParameters::outputTiming

Definition at line 875 of file SimParameters.h.

Referenced by Controller::printTiming().

int SimParameters::pairInteractionGroup1

Definition at line 535 of file SimParameters.h.

int SimParameters::pairInteractionGroup2

Definition at line 536 of file SimParameters.h.

Bool SimParameters::pairInteractionOn

Definition at line 534 of file SimParameters.h.

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

Bool SimParameters::pairInteractionSelf

Definition at line 537 of file SimParameters.h.

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

BigReal SimParameters::pairlistDist

Definition at line 238 of file SimParameters.h.

BigReal SimParameters::pairlistGrow

Definition at line 246 of file SimParameters.h.

int SimParameters::pairlistMinProcs

Definition at line 240 of file SimParameters.h.

BigReal SimParameters::pairlistShrink

Definition at line 245 of file SimParameters.h.

int SimParameters::pairlistsPerCycle

Definition at line 244 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects().

BigReal SimParameters::pairlistTrigger

Definition at line 247 of file SimParameters.h.

Bool SimParameters::paraTypeCharmmOn

Definition at line 284 of file SimParameters.h.

Referenced by ParallelIOMgr::bcastHydroBasedCounter(), and NamdState::loadStructure().

Bool SimParameters::paraTypeXplorOn

Definition at line 283 of file SimParameters.h.

Referenced by ParallelIOMgr::bcastHydroBasedCounter(), and NamdState::loadStructure().

BigReal SimParameters::patchDimension

Definition at line 221 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::PMEBarrier

Definition at line 765 of file SimParameters.h.

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 756 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::PMEGridSizeX

Definition at line 758 of file SimParameters.h.

int SimParameters::PMEGridSizeY

Definition at line 759 of file SimParameters.h.

int SimParameters::PMEGridSizeZ

Definition at line 760 of file SimParameters.h.

BigReal SimParameters::PMEGridSpacing

Definition at line 761 of file SimParameters.h.

int SimParameters::PMEInterpOrder

Definition at line 757 of file SimParameters.h.

int SimParameters::PMEMinPoints

Definition at line 764 of file SimParameters.h.

int SimParameters::PMEMinSlices

Definition at line 763 of file SimParameters.h.

Bool SimParameters::PMEOffload

Definition at line 773 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA().

Bool SimParameters::PMEOn

Definition at line 754 of file SimParameters.h.

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

int SimParameters::PMEPencils

Definition at line 766 of file SimParameters.h.

int SimParameters::PMEPencilsX

Definition at line 767 of file SimParameters.h.

int SimParameters::PMEPencilsXLayout

Definition at line 771 of file SimParameters.h.

int SimParameters::PMEPencilsY

Definition at line 768 of file SimParameters.h.

int SimParameters::PMEPencilsYLayout

Definition at line 770 of file SimParameters.h.

int SimParameters::PMEPencilsZ

Definition at line 769 of file SimParameters.h.

int SimParameters::PMEProcessors

Definition at line 762 of file SimParameters.h.

int SimParameters::PMESendOrder

Definition at line 772 of file SimParameters.h.

BigReal SimParameters::PMETolerance

Definition at line 755 of file SimParameters.h.

int SimParameters::pressureProfileAtomTypes

Definition at line 692 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< AnisoElem, aniso, aniso >::ComputeHomeTuples(), Controller::Controller(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), and Sequencer::Sequencer().

Bool SimParameters::pressureProfileEwaldOn

Definition at line 693 of file SimParameters.h.

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

int SimParameters::pressureProfileEwaldX

Definition at line 694 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldY

Definition at line 695 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldZ

Definition at line 696 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileFreq

Definition at line 691 of file SimParameters.h.

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

Bool SimParameters::pressureProfileOn

Definition at line 689 of file SimParameters.h.

Referenced by ComputeHomeTuples< AnisoElem, aniso, aniso >::ComputeHomeTuples(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), Controller::Controller(), and Sequencer::Sequencer().

int SimParameters::pressureProfileSlabs

Definition at line 690 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< AnisoElem, aniso, aniso >::ComputeHomeTuples(), Controller::Controller(), Sequencer::Sequencer(), and Sequencer::submitHalfstep().

Bool SimParameters::printBadContacts

Definition at line 506 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Bool SimParameters::printExclusions

Definition at line 1002 of file SimParameters.h.

int SimParameters::proxyRecvSpanningTree

Definition at line 1006 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

int SimParameters::proxySendSpanningTree

Definition at line 1005 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

int SimParameters::proxyTreeBranchFactor

Definition at line 1008 of file SimParameters.h.

Referenced by Node::startup().

char SimParameters::qmBaseDir[256]

Definition at line 464 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmBondColumn[16]

Definition at line 474 of file SimParameters.h.

Bool SimParameters::qmBondDist

Definition at line 475 of file SimParameters.h.

Bool SimParameters::qmBondOn

Definition at line 473 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmBondScheme

Definition at line 479 of file SimParameters.h.

char SimParameters::qmBondSchemeS[16]

Definition at line 478 of file SimParameters.h.

int SimParameters::qmBondValType

Definition at line 476 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmBondValueTypeS[16]

Definition at line 477 of file SimParameters.h.

Bool SimParameters::qmChrgFromPSF

Definition at line 458 of file SimParameters.h.

int SimParameters::qmChrgMode

Definition at line 462 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmChrgModeS[16]

Definition at line 461 of file SimParameters.h.

char SimParameters::qmColumn[16]

Definition at line 463 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmCSMD

Definition at line 499 of file SimParameters.h.

char SimParameters::qmCSMDFile[128]

Definition at line 500 of file SimParameters.h.

Bool SimParameters::qmCustomPCSel

Definition at line 491 of file SimParameters.h.

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

Bool SimParameters::qmElecEmbed

Definition at line 489 of file SimParameters.h.

int SimParameters::qmEnergyOutFreq

Definition at line 502 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

char SimParameters::qmExecPath[256]

Definition at line 459 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmForcesOn

Definition at line 455 of file SimParameters.h.

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

int SimParameters::qmFormat

Definition at line 469 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmLSSFreq

Definition at line 494 of file SimParameters.h.

int SimParameters::qmLSSMode

Definition at line 497 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmLSSModeS[16]

Definition at line 496 of file SimParameters.h.

Bool SimParameters::qmLSSOn

Definition at line 493 of file SimParameters.h.

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

char SimParameters::qmLSSResname[5]

Definition at line 495 of file SimParameters.h.

Bool SimParameters::qmMOPACAddConfigChrg

Definition at line 471 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmNoPC

Definition at line 488 of file SimParameters.h.

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

int SimParameters::qmOutFreq

Definition at line 503 of file SimParameters.h.

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

char SimParameters::qmParamPDB[128]

Definition at line 456 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::qmParamPDBDefined

Definition at line 457 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::qmPCScheme

Definition at line 484 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSchemeS[16]

Definition at line 483 of file SimParameters.h.

int SimParameters::qmPCSelFreq

Definition at line 490 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmPCSwitchOn

Definition at line 480 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmPCSwitchType

Definition at line 482 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSwitchTypeS[16]

Definition at line 481 of file SimParameters.h.

int SimParameters::qmPosOutFreq

Definition at line 504 of file SimParameters.h.

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

char SimParameters::qmPrepProc[256]

Definition at line 467 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmPrepProcOn

Definition at line 468 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmReplaceAll

Definition at line 470 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::qmSecProc[256]

Definition at line 465 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmSecProcOn

Definition at line 466 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmSimsPerNode

Definition at line 485 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmSoftware[128]

Definition at line 460 of file SimParameters.h.

Bool SimParameters::qmVDW

Definition at line 487 of file SimParameters.h.

unsigned int SimParameters::randomSeed

Definition at line 701 of file SimParameters.h.

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

Bool SimParameters::readExclusions

Definition at line 976 of file SimParameters.h.

Referenced by buildExclusions().

int SimParameters::reassignFreq

Definition at line 646 of file SimParameters.h.

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

BigReal SimParameters::reassignHold

Definition at line 649 of file SimParameters.h.

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

BigReal SimParameters::reassignIncr

Definition at line 648 of file SimParameters.h.

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

BigReal SimParameters::reassignTemp

Definition at line 647 of file SimParameters.h.

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

Bool SimParameters::replicaUniformPatchGrids

Definition at line 936 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::rescaleFreq

Definition at line 598 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 599 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 210 of file SimParameters.h.

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

int SimParameters::restartFrequency

Definition at line 211 of file SimParameters.h.

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

Bool SimParameters::restartSave

Definition at line 213 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::restartSaveDcd

Definition at line 214 of file SimParameters.h.

int SimParameters::rigidBonds

Definition at line 904 of file SimParameters.h.

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

int SimParameters::rigidDie

Definition at line 909 of file SimParameters.h.

int SimParameters::rigidIter

Definition at line 908 of file SimParameters.h.

BigReal SimParameters::rigidTol

Definition at line 907 of file SimParameters.h.

zVector SimParameters::rotConsAxis

Definition at line 304 of file SimParameters.h.

zVector SimParameters::rotConsPivot

Definition at line 305 of file SimParameters.h.

Bool SimParameters::rotConstraintsOn

Definition at line 302 of file SimParameters.h.

BigReal SimParameters::rotConsVel

Definition at line 306 of file SimParameters.h.

char SimParameters::rotDragAxisFile[128]

Definition at line 321 of file SimParameters.h.

char SimParameters::rotDragFile[128]

Definition at line 319 of file SimParameters.h.

BigReal SimParameters::rotDragGlobVel

Definition at line 323 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

Bool SimParameters::rotDragOn

Definition at line 318 of file SimParameters.h.

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

char SimParameters::rotDragPivotFile[128]

Definition at line 322 of file SimParameters.h.

char SimParameters::rotDragVelFile[128]

Definition at line 324 of file SimParameters.h.

BigReal SimParameters::scale14

Definition at line 188 of file SimParameters.h.

BigReal SimParameters::scriptArg1

Definition at line 986 of file SimParameters.h.

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

BigReal SimParameters::scriptArg2

Definition at line 987 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg3

Definition at line 988 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg4

Definition at line 989 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg5

Definition at line 990 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::scriptIntArg1

Definition at line 991 of file SimParameters.h.

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

int SimParameters::scriptIntArg2

Definition at line 992 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::scriptStringArg1[128]

Definition at line 993 of file SimParameters.h.

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

char SimParameters::scriptStringArg2[128]

Definition at line 994 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::selectConstraintsOn

Definition at line 269 of file SimParameters.h.

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 341 of file SimParameters.h.

char SimParameters::SMDFile[128]

Definition at line 344 of file SimParameters.h.

BigReal SimParameters::SMDk

Definition at line 342 of file SimParameters.h.

BigReal SimParameters::SMDk2

Definition at line 343 of file SimParameters.h.

Bool SimParameters::SMDOn

Definition at line 339 of file SimParameters.h.

int SimParameters::SMDOutputFreq

Definition at line 345 of file SimParameters.h.

BigReal SimParameters::SMDVel

Definition at line 340 of file SimParameters.h.

Bool SimParameters::soluteScalingAll

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

Definition at line 446 of file SimParameters.h.

Referenced by ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples().

BigReal SimParameters::soluteScalingFactor

scaling factor for solute interactions

Definition at line 438 of file SimParameters.h.

Referenced by ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples(), and scriptSet().

BigReal SimParameters::soluteScalingFactorCharge

optional independent control over scaling factor for electrostatic interactions of solute

Definition at line 440 of file SimParameters.h.

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

BigReal SimParameters::soluteScalingFactorVdw

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

Definition at line 443 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::soluteScalingOn

REST2 (replica exchange solute tempering) on?

Definition at line 436 of file SimParameters.h.

Referenced by LJTable::LJTable(), NamdState::loadStructure(), ComputeHomeTuples< AnisoElem, aniso, aniso >::loadTuples(), Molecule::receive_Molecule(), Molecule::send_Molecule(), and Sequencer::Sequencer().

BigReal SimParameters::solvent_dielectric

Definition at line 512 of file SimParameters.h.

int SimParameters::sphericalBCexp1

Definition at line 832 of file SimParameters.h.

int SimParameters::sphericalBCexp2

Definition at line 833 of file SimParameters.h.

BigReal SimParameters::sphericalBCk1

Definition at line 826 of file SimParameters.h.

BigReal SimParameters::sphericalBCk2

Definition at line 828 of file SimParameters.h.

Bool SimParameters::sphericalBCOn

Definition at line 823 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::sphericalBCr1

Definition at line 830 of file SimParameters.h.

BigReal SimParameters::sphericalBCr2

Definition at line 831 of file SimParameters.h.

zVector SimParameters::sphericalCenter

Definition at line 825 of file SimParameters.h.

Bool SimParameters::sphericalConstraintsOn

Definition at line 277 of file SimParameters.h.

zVector SimParameters::sphericalConstrCenter

Definition at line 278 of file SimParameters.h.

int SimParameters::splitPatch

Definition at line 897 of file SimParameters.h.

Bool SimParameters::staticAtomAssignment

Definition at line 935 of file SimParameters.h.

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

Bool SimParameters::statsOn

Definition at line 915 of file SimParameters.h.

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

int SimParameters::stepsPerCycle

Definition at line 114 of file SimParameters.h.

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

zVector SimParameters::stirAxis

Definition at line 860 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::stirFilename[128]

Definition at line 855 of file SimParameters.h.

BigReal SimParameters::stirK

Definition at line 859 of file SimParameters.h.

Bool SimParameters::stirOn

Definition at line 854 of file SimParameters.h.

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

zVector SimParameters::stirPivot

Definition at line 861 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::stirStartingTheta

Definition at line 857 of file SimParameters.h.

BigReal SimParameters::stirVel

Definition at line 858 of file SimParameters.h.

int SimParameters::stochRescaleFreq

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 596 of file SimParameters.h.

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

Bool SimParameters::stochRescaleOn

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

Definition at line 583 of file SimParameters.h.

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

BigReal SimParameters::stochRescalePeriod

Timescale (ps) for stochastic velocity rescaling.

Definition at line 593 of file SimParameters.h.

Referenced by Controller::Controller().

BigReal SimParameters::stochRescaleTemp

Temperature for stochastic velocity rescaling.

Definition at line 590 of file SimParameters.h.

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

Bool SimParameters::storeComputeMap

Definition at line 1023 of file SimParameters.h.

zVector SimParameters::strainRate

Definition at line 698 of file SimParameters.h.

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

zVector SimParameters::strainRate2

Definition at line 699 of file SimParameters.h.

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

BigReal SimParameters::surface_tension

Definition at line 522 of file SimParameters.h.

BigReal SimParameters::surfaceTensionTarget

Definition at line 687 of file SimParameters.h.

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

Bool SimParameters::switchingActive

Definition at line 228 of file SimParameters.h.

BigReal SimParameters::switchingDist

Definition at line 232 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::symmetryFile[128]

Definition at line 369 of file SimParameters.h.

int SimParameters::symmetryFirstFullStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryFirstStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

BigReal SimParameters::symmetryk

Definition at line 367 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetrykfile[128]

Definition at line 368 of file SimParameters.h.

int SimParameters::symmetryLastFullStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryLastStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetryMatrixFile[128]

Definition at line 370 of file SimParameters.h.

Bool SimParameters::symmetryOn

Definition at line 366 of file SimParameters.h.

Bool SimParameters::symmetryScaleForces

Definition at line 366 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::tableInterpType[128]

Definition at line 352 of file SimParameters.h.

BigReal SimParameters::tableMaxDist

Definition at line 354 of file SimParameters.h.

int SimParameters::tableNumTypes

Definition at line 350 of file SimParameters.h.

Real SimParameters::tableSpacing

Definition at line 353 of file SimParameters.h.

Bool SimParameters::tabulatedEnergies

Definition at line 349 of file SimParameters.h.

char SimParameters::tabulatedEnergiesFile[128]

Definition at line 351 of file SimParameters.h.

char SimParameters::tclBCArgs[128]

Definition at line 547 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::tclBCOn

Definition at line 545 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

char* SimParameters::tclBCScript

Definition at line 546 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Bool SimParameters::tclForcesOn

Definition at line 541 of file SimParameters.h.

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

Bool SimParameters::tclIsThreaded

Definition at line 543 of file SimParameters.h.

Bool SimParameters::tCoupleOn

Definition at line 578 of file SimParameters.h.

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

BigReal SimParameters::tCoupleTemp

Definition at line 580 of file SimParameters.h.

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

Bool SimParameters::testOn

Definition at line 913 of file SimParameters.h.

Bool SimParameters::TMDDiffRMSD

Definition at line 358 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile[128]

Definition at line 360 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile2[128]

Definition at line 360 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDFinalRMSD

Definition at line 363 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDFirstStep

Definition at line 362 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDInitialRMSD

Definition at line 363 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDk

Definition at line 359 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDLastStep

Definition at line 362 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Bool SimParameters::TMDOn

Definition at line 358 of file SimParameters.h.

int SimParameters::TMDOutputFreq

Definition at line 361 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::totalAtoms

Definition at line 917 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 164 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayY

Definition at line 165 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayZ

Definition at line 166 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::useAntecedent

Definition at line 947 of file SimParameters.h.

int SimParameters::useCkLoop

Definition at line 162 of file SimParameters.h.

Referenced by PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), PmeXPencil::forward_fft(), PmeYPencil::forward_fft(), PmeZPencil::forward_fft(), ComputePmeCUDADevice::gatherForceDone(), PmeZPencil::send_all_ungrid(), PmeYPencil::send_trans(), PmeZPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), and Node::startup().

Bool SimParameters::useCompressedPsf

Definition at line 996 of file SimParameters.h.

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

Bool SimParameters::useConstantArea

Definition at line 657 of file SimParameters.h.

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

Bool SimParameters::useConstantRatio

Definition at line 658 of file SimParameters.h.

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

Bool SimParameters::useCUDA2

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

Definition at line 782 of file SimParameters.h.

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

Bool SimParameters::useCUDAdisable

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

Definition at line 793 of file SimParameters.h.

Bool SimParameters::useDPME

Definition at line 775 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::useFlexibleCell

Definition at line 656 of file SimParameters.h.

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

Bool SimParameters::useGroupPressure

Definition at line 651 of file SimParameters.h.

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

Bool SimParameters::useManyToMany

Definition at line 801 of file SimParameters.h.

Bool SimParameters::useOptPME

Definition at line 800 of file SimParameters.h.

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

int SimParameters::usePairlists

Definition at line 242 of file SimParameters.h.

Bool SimParameters::usePluginIO

Definition at line 999 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::usePMECUDA

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

Definition at line 778 of file SimParameters.h.

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

Bool SimParameters::useSettle

Definition at line 911 of file SimParameters.h.

Bool SimParameters::vdwForceSwitching

Definition at line 230 of file SimParameters.h.

Bool SimParameters::vdwGeometricSigma

Definition at line 983 of file SimParameters.h.

BigReal SimParameters::vdwscale14

Definition at line 977 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::velDcdFilename[128]

Definition at line 202 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::velDcdFrequency

Definition at line 194 of file SimParameters.h.

Bool SimParameters::verboseTopology

Definition at line 154 of file SimParameters.h.

int SimParameters::watmodel

Definition at line 109 of file SimParameters.h.

Bool SimParameters::wrapAll

Definition at line 183 of file SimParameters.h.

Referenced by ParallelIOMgr::integrateClusterSize(), ParallelIOMgr::readPerAtomInfo(), ParallelIOMgr::recvFinalClusterCoor(), and colvarproxy_namd::setup().

Bool SimParameters::wrapNearest

Definition at line 184 of file SimParameters.h.

Referenced by ParallelIOMgr::recvFinalClusterCoor().

Bool SimParameters::wrapWater

Definition at line 182 of file SimParameters.h.

Referenced by ParallelIOMgr::integrateClusterSize(), and ParallelIOMgr::readPerAtomInfo().

char SimParameters::xstFilename[128]

Definition at line 204 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

int SimParameters::xstFrequency

Definition at line 198 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::zeroMomentum

Definition at line 180 of file SimParameters.h.

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

Bool SimParameters::zeroMomentumAlt

Definition at line 181 of file SimParameters.h.

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


The documentation for this class was generated from the following files:
Generated on Sat Sep 22 01:17:21 2018 for NAMD by  doxygen 1.4.7