SimParameters Class Reference

#include <SimParameters.h>

List of all members.

Public Member Functions

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

Static Public Member Functions

static void nonbonded_select ()
static void pme_select ()

Public Attributes

Bool lonepairs
int watmodel
Bool LJcorrection
BigReal dt
int N
int stepsPerCycle
zVector cellBasisVector1
zVector cellBasisVector2
zVector cellBasisVector3
zVector cellOrigin
Lattice lattice
int nonbondedFrequency
int fullElectFrequency
BigReal fmaTheta
int ldBalancer
int ldbStrategy
int ldbPeriod
int firstLdbStep
int lastLdbStep
int hybridGroupSize
BigReal ldbBackgroundScaling
BigReal ldbPMEBackgroundScaling
BigReal ldbHomeBackgroundScaling
BigReal ldbRelativeGrainsize
int traceStartStep
int numTraceSteps
Bool outputMaps
Bool simulateInitialMapping
int simulatedPEs
int simulatedNodeSize
Bool disableTopology
Bool verboseTopology
Bool benchTimestep
int useCkLoop
int twoAwayX
int twoAwayY
int twoAwayZ
int maxPatches
Bool ldbUnloadPME
Bool ldbUnloadZero
Bool ldbUnloadOne
Bool ldbUnloadOutputPEs
Bool noPatchesOnZero
Bool noPatchesOnOutputPEs
Bool noPatchesOnOne
BigReal initialTemp
Bool comMove
Bool zeroMomentum
Bool zeroMomentumAlt
Bool wrapWater
Bool wrapAll
Bool wrapNearest
BigReal dielectric
ExclusionSettings exclude
BigReal scale14
BigReal nonbondedScaling
int dcdFrequency
int dcdUnitCell
int velDcdFrequency
int forceDcdFrequency
int xstFrequency
char auxFilename [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 alchWCAOn
int alchMethod
BigReal alchLambda
BigReal alchLambda2
BigReal alchLambdaIDWS
int alchIDWSFreq
int alchLambdaFreq
BigReal alchTemp
int alchOutFreq
Bool alchEnsembleAvg
char alchOutFile [128]
int alchEquilSteps
BigReal alchVdwShiftCoeff
BigReal alchElecLambdaStart
BigReal alchVdwLambdaEnd
BigReal alchRepLambdaEnd
BigReal alchBondLambdaEnd
Bool alchDecouple
Bool alchBondDecouple
Bool lesOn
int lesFactor
Bool lesReduceTemp
Bool lesReduceMass
Bool soluteScalingOn
BigReal soluteScalingFactor
BigReal soluteScalingFactorCharge
BigReal soluteScalingFactorVdw
Bool soluteScalingAll
Bool extForcesOn
char extForcesCommand [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
Bool stochRescaleHeat
int rescaleFreq
BigReal rescaleTemp
Bool accelMDOn
Bool accelMDdihe
Bool accelMDdual
Bool accelMDDebugOn
BigReal accelMDFirstStep
BigReal accelMDLastStep
int accelMDOutFreq
BigReal accelMDE
BigReal accelMDalpha
BigReal accelMDTE
BigReal accelMDTalpha
Bool accelMDG
int accelMDGiE
int accelMDGcMDSteps
int accelMDGEquiSteps
int accelMDGcMDPrepSteps
int accelMDGEquiPrepSteps
int accelMDGStatWindow
BigReal accelMDGSigma0P
BigReal accelMDGSigma0D
Bool accelMDGRestart
char accelMDGRestartFile [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 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 extraBondsCosAngles
Bool extraBondsCosAnglesSetByUser
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 1050 of file SimParameters.h.

01050 : mgridforcelist(), parseopts(0) {};

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

Definition at line 1051 of file SimParameters.h.

References initialize_config_data().

01051                                                  : mgridforcelist(), parseopts(0) {
01052           initialize_config_data(c,cwd);
01053         };

SimParameters::~SimParameters (  )  [inline]

Definition at line 1054 of file SimParameters.h.

01054 {};


Member Function Documentation

void SimParameters::close_dcdfile (  ) 

Definition at line 655 of file Output.C.

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

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(), and Node::output.

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  lambda  ) 

Definition at line 7201 of file SimParameters.C.

References alchBondLambdaEnd.

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

07201                                                          {
07202   // Convenience function for staggered lambda scaling
07203   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
07204 }

BigReal SimParameters::getCurrentLambda ( const int  step  ) 

Definition at line 7122 of file SimParameters.C.

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

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

07122                                                       {
07123   /*Get lambda at the current step. 
07124 
07125    If alchLambdaFreq = 0, return alchLambda. For positive values of 
07126    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
07127    alchLambda2:
07128 
07129    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
07130 
07131    n - the current time step
07132    n0 - step at which switching begins (default = 0)
07133    N - total steps in the simulation
07134    dn - alchLambdaFreq (increment frequency, in steps)
07135    l/l2 - alchLambda/alchLambda2
07136  
07137    Note that each step _begins_ by incrementing alchLambda and then integrates
07138    in time. This means that the first and last switch steps may not behave as
07139    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
07140    no step occurs because alchLambda2 has already been reached.
07141   */
07142   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
07143     if ( step == N ) {
07144       return alchLambda2;
07145     }
07146     else {
07147       const int timeOrigin = firstTimestep + alchEquilSteps;
07148       const BigReal alchLambdaDelta = getLambdaDelta();
07149       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
07150       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
07151     }
07152   }
07153   else {
07154     return alchLambda;
07155   }
07156 }

BigReal SimParameters::getCurrentLambda2 ( const int  step  ) 
BigReal SimParameters::getElecLambda ( const BigReal  lambda  ) 

Definition at line 7164 of file SimParameters.C.

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

07164                                                          {
07165   // Convenience function for staggered lambda scaling
07166   return (lambda <= alchElecLambdaStart ? 0.
07167           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
07168 }

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 7158 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, and firstTimestep.

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

07158                                           {
07159   // Increment by which Lambda changes.
07160   return ((alchLambda2 - alchLambda)*alchLambdaFreq
07161           / BigReal(N - firstTimestep - alchEquilSteps));
07162 }

BigReal SimParameters::getRepLambda ( const BigReal  lambda  ) 

Definition at line 7196 of file SimParameters.C.

References alchRepLambdaEnd.

07196                                                         {
07197   // Convenience function for staggered lambda scaling
07198   return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd);
07199 }

BigReal SimParameters::getVdwLambda ( const BigReal  lambda  ) 

Definition at line 7178 of file SimParameters.C.

References alchRepLambdaEnd, alchVdwLambdaEnd, and alchWCAOn.

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

07178                                                         {
07179   // Convenience function for staggered lambda scaling
07180   if ( alchWCAOn ) {
07181     // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart.
07182     // The second condition is needed when attractive interactions are inactive
07183     // for the whole range, otherwise lambda = 0/1 are incorrect.
07184     if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) {
07185       return 0.0;
07186     } else if ( lambda >= alchVdwLambdaEnd ) {
07187       return 1.0;
07188     } else {
07189       return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd);
07190     }
07191   } else {
07192     return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
07193   }
07194 }

void SimParameters::initialize_config_data ( ConfigList config,
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 1076 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

01076 { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (  )  [inline]

Definition at line 1077 of file SimParameters.h.

References proxyRecvSpanningTree.

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

01077 { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (  )  [inline]

Definition at line 1074 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

01074 { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (  )  [inline]

Definition at line 1075 of file SimParameters.h.

References proxySendSpanningTree.

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

01075 { 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 392 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

00392                                      {
00393     ComputeNonbondedUtil::select();
00394 }

void SimParameters::pme_select (  )  [static]

Definition at line 396 of file SimParameters.C.

References ComputePmeUtil::select().

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

00396                                {
00397   ComputePmeUtil::select();
00398 }

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

Definition at line 2313 of file SimParameters.C.

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

02313                                                                             {
02314 
02315      if ( ! latptr ) {
02316        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
02317      }
02318 
02319      ifstream xscFile(filename);
02320      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
02321 
02322      char labels[1024];
02323      do {
02324        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02325        xscFile.getline(labels,1023);
02326      } while ( strncmp(labels,"#$LABELS ",9) );
02327 
02328      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
02329      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
02330      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
02331      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
02332 
02333      int pos = 0;
02334      char *l_i = labels + 8;
02335      while ( *l_i ) {
02336        if ( *l_i == ' ' ) { ++l_i; continue; }
02337        char *l_i2;
02338        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
02339        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
02340          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
02341          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
02342          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
02343          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
02344          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
02345          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
02346          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
02347          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
02348          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
02349          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
02350          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
02351          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
02352          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
02353          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
02354          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
02355          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
02356          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
02357          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
02358        }
02359        ++pos;
02360        l_i = l_i2;
02361      }
02362      int numpos = pos;
02363 
02364      for ( pos = 0; pos < numpos; ++pos ) {
02365        double tmp;
02366        xscFile >> tmp;
02367        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02368        if ( pos == a_x ) cellBasisVector1.x = tmp;
02369        if ( pos == a_y ) cellBasisVector1.y = tmp;
02370        if ( pos == a_z ) cellBasisVector1.z = tmp;
02371        if ( pos == b_x ) cellBasisVector2.x = tmp;
02372        if ( pos == b_y ) cellBasisVector2.y = tmp;
02373        if ( pos == b_z ) cellBasisVector2.z = tmp;
02374        if ( pos == c_x ) cellBasisVector3.x = tmp;
02375        if ( pos == c_y ) cellBasisVector3.y = tmp;
02376        if ( pos == c_z ) cellBasisVector3.z = tmp;
02377        if ( pos == o_x ) cellOrigin.x = tmp;
02378        if ( pos == o_y ) cellOrigin.y = tmp;
02379        if ( pos == o_z ) cellOrigin.z = tmp;
02380        if ( pos == s_u ) strainRate2.x = tmp;
02381        if ( pos == s_v ) strainRate2.y = tmp;
02382        if ( pos == s_w ) strainRate2.z = tmp;
02383        if ( pos == s_x ) strainRate.x = tmp;
02384        if ( pos == s_y ) strainRate.y = tmp;
02385        if ( pos == s_z ) strainRate.z = tmp;
02386      }
02387 
02388    if ( latptr ) {
02389      Lattice test;
02390      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02391     
02392      if ( test.a_p() && ! lattice.a_p() ) {
02393        NAMD_die("cellBasisVector1 added during atom reinitialization");
02394      }
02395      if ( lattice.a_p() && ! test.a_p() ) {
02396        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
02397      }
02398      if ( test.b_p() && ! lattice.b_p() ) {
02399        NAMD_die("cellBasisVector2 added during atom reinitialization");
02400      }
02401      if ( lattice.b_p() && ! test.b_p() ) {
02402        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
02403      }
02404      if ( test.c_p() && ! lattice.c_p() ) {
02405        NAMD_die("cellBasisVector3 added during atom reinitialization");
02406      }
02407      if ( lattice.c_p() && ! test.c_p() ) {
02408        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
02409      }
02410 
02411      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02412    }
02413 
02414 }

void SimParameters::receive_SimParameters ( MIStream msg  ) 

Definition at line 7025 of file SimParameters.C.

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

07027 {
07028   msg->get(sizeof(SimParameters),(char*)this);
07029   if ( FFTWWisdomString ) {
07030     int fftwlen;
07031     msg->get(fftwlen);
07032     FFTWWisdomString = new char[fftwlen];
07033     msg->get(fftwlen,FFTWWisdomString);
07034 #ifdef NAMD_FFTW
07035 #ifdef NAMD_FFTW_3
07036     fftwf_import_wisdom_from_string(FFTWWisdomString);
07037 #else
07038     fftw_import_wisdom_from_string(FFTWWisdomString);
07039 #endif
07040 #endif
07041   }
07042   if ( tclBCScript ) {
07043     int tcllen;
07044     msg->get(tcllen);
07045     tclBCScript = new char[tcllen];
07046     msg->get(tcllen,tclBCScript);
07047   }
07048 
07049 #ifdef MEM_OPT_VERSION
07050   int filelen;
07051   msg->get(filelen);
07052   binAtomFile = new char[filelen];
07053   msg->get(filelen, binAtomFile);
07054   
07055   msg->get(filelen);
07056   binCoorFile = new char[filelen];
07057   msg->get(filelen, binCoorFile);
07058 
07059   if(binVelFile) {    
07060     msg->get(filelen);
07061     binVelFile = new char[filelen];
07062     msg->get(filelen, binVelFile);
07063   }
07064 
07065   if(binRefFile) {    
07066     msg->get(filelen);
07067     binRefFile = new char[filelen];
07068     msg->get(filelen, binRefFile);
07069   }
07070 #endif
07071 
07072 
07073   // The simParameters bit copy above put illegal values in the list pointers
07074   // So this resets everything so that unpacking will work.
07075   mgridforcelist.clear();
07076   mgridforcelist.unpack_data(msg);
07077   
07078   delete msg;
07079 }

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

Definition at line 169 of file SimParameters.C.

References accelMDalpha, accelMDE, accelMDGRestartFile, accelMDGSigma0D, accelMDGSigma0P, accelMDTalpha, accelMDTE, alchEquilSteps, alchFepOn, alchFepOnAtStartup, alchLambda, alchLambda2, alchLambdaFreq, alchLambdaIDWS, alchOn, alchOnAtStartup, 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, ComputeCUDAMgr::getComputeCUDAMgr(), initialTemp, langevin_useBAOAB, langevinOn, langevinOnAtStartup, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, maximumMove, minimizeOn, N, NAMD_die(), 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(), setupIDWS(), 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,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00300     alchLambda = atof(value);
00301     if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
00302       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00303     }
00304     ComputeNonbondedUtil::select();
00305     return;
00306   }
00307 
00308   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00309     alchLambda2 = atof(value);
00310     if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
00311       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00312     }
00313     ComputeNonbondedUtil::select();
00314     return;
00315   }
00316 
00317   if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
00318     alchLambdaIDWS = atof(value);
00319     setupIDWS();
00320     ComputeNonbondedUtil::select();
00321     return;
00322   }
00323 
00324   if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
00325     alchLambdaFreq = atoi(value);
00326     if ( alchLambdaIDWS >= 0 ) {
00327       NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n");
00328     }
00329     ComputeNonbondedUtil::select();
00330     return;
00331   }
00332 //fepe
00333 
00334   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00335     nonbondedScaling = atof(value);
00336     ComputeNonbondedUtil::select();
00337     return;
00338   }
00339 
00340   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00341     commOnly = atobool(value);
00342     ComputeNonbondedUtil::select();
00343     return;
00344   }
00345 
00346   // REST2 - We don't have to make any changes to ComputeNonbondedUtil
00347   // other than recalculating the LJTable.  Skip doing the other stuff.
00348   if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) {
00349     soluteScalingFactor = atof(value);
00350     if (soluteScalingFactor < 0.0) {
00351       NAMD_die("Solute scaling factor should be non-negative\n");
00352     }
00353     soluteScalingFactorCharge = soluteScalingFactor;
00354     soluteScalingFactorVdw = soluteScalingFactor;
00355     // update LJTable for CPU
00356     ComputeNonbondedUtil::select();
00357 #ifdef NAMD_CUDA
00358     // update LJTable for GPU, needs CPU update first
00359     ComputeCUDAMgr::getComputeCUDAMgr()->update();
00360 #endif
00361     return;
00362   }
00363   if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) {
00364     soluteScalingFactorVdw = atof(value);
00365     if (soluteScalingFactorVdw < 0.0) {
00366       NAMD_die("Solute scaling factor for van der Waals "
00367           "should be non-negative\n");
00368     }
00369     // update LJTable for CPU
00370     ComputeNonbondedUtil::select();
00371 #ifdef NAMD_CUDA
00372     // update LJTable for GPU, needs CPU update first
00373     ComputeCUDAMgr::getComputeCUDAMgr()->update();
00374 #endif
00375     return;
00376   }
00377   if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) {
00378     soluteScalingFactorCharge = atof(value);
00379     if (soluteScalingFactorCharge < 0.0) {
00380       NAMD_die("Solute scaling factor for electrostatics "
00381           "should be non-negative\n");
00382     }
00383     return;
00384   }
00385 
00386   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00387   sprintf(error,"Setting parameter %s from script failed!\n",param);
00388   NAMD_die(error);
00389 
00390 }

void SimParameters::send_SimParameters ( MOStream msg  ) 

Definition at line 6967 of file SimParameters.C.

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

06969 {
06970   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
06971   if ( msg == NULL )
06972   {
06973     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
06974   }*/
06975 
06976   msg->put(sizeof(SimParameters),(char*)this);
06977   if ( FFTWWisdomString ) {
06978     int fftwlen = strlen(FFTWWisdomString) + 1;
06979     msg->put(fftwlen);
06980     msg->put(fftwlen,FFTWWisdomString);
06981   }
06982   if ( tclBCScript ) {
06983     int tcllen = strlen(tclBCScript) + 1;
06984     msg->put(tcllen);
06985     msg->put(tcllen,tclBCScript);
06986   }
06987 
06988 #ifdef MEM_OPT_VERSION
06989   int filelen = strlen(binAtomFile)+1;
06990   msg->put(filelen);
06991   msg->put(filelen, binAtomFile);
06992 
06993   filelen = strlen(binCoorFile)+1;
06994   msg->put(filelen);
06995   msg->put(filelen, binCoorFile);
06996 
06997   if(binVelFile) {
06998     filelen = strlen(binVelFile)+1;
06999     msg->put(filelen);
07000     msg->put(filelen, binVelFile);
07001   }
07002 
07003   if(binRefFile) {
07004     filelen = strlen(binRefFile)+1;
07005     msg->put(filelen);
07006     msg->put(filelen, binRefFile);
07007   }
07008 #endif
07009 
07010   mgridforcelist.pack_data(msg);
07011   
07012   msg->end();
07013 }

int SimParameters::setupIDWS (  ) 

Definition at line 7094 of file SimParameters.C.

References alchIDWSFreq, alchLambdaIDWS, alchOutFreq, iout, iWARN(), NAMD_die(), and outputEnergies.

Referenced by scriptSet().

07094                              {
07095   if (alchLambdaIDWS < 0.) return 0;
07096   if (alchLambdaIDWS > 1.) {
07097     NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
07098   }
07099  /* 
07100   * The internal parameter alchIDWSFreq determines the number of steps of MD
07101   * before each switch of the value of alchLambda2. At most this occurs every
07102   * time the energy is evaluated and thus the default is the greater of
07103   * fullElectFrequency and nonbondedFrequency. However, this choice fails to
07104   * report alternating values if output is printed less often than every step
07105   * (which is almost certainly true). Thus the frequency is reset to match
07106   * alchOutFreq or, if that is zero, outputEnergies. Note that, if 
07107   * alchOutFreq > 0 but != outputEnergies, then the data going to stdout
07108   * are likely not useful since the comparison value is difficult to infer.
07109   */
07110   alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency;
07111   if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies;
07112   if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq;
07113   if ( alchOutFreq && alchOutFreq != outputEnergies) {
07114     iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput"
07115          << " to stdout may not be useful!\n" << endi;
07116   }
07117   return 1;
07118 }


Member Data Documentation

Definition at line 967 of file SimParameters.h.

Definition at line 623 of file SimParameters.h.

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

Definition at line 622 of file SimParameters.h.

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

Definition at line 619 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 627 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 631 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 629 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 632 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 630 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 628 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 638 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 636 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 637 of file SimParameters.h.

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

Definition at line 635 of file SimParameters.h.

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

Definition at line 634 of file SimParameters.h.

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

Definition at line 633 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 620 of file SimParameters.h.

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

Definition at line 621 of file SimParameters.h.

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

Definition at line 625 of file SimParameters.h.

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

Definition at line 624 of file SimParameters.h.

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

Definition at line 649 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 650 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 652 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 642 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 651 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 643 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

Definition at line 646 of file SimParameters.h.

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

Definition at line 655 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 645 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 658 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 654 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

Definition at line 656 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 648 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 647 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 434 of file SimParameters.h.

Referenced by CrosstermElem::computeForce().

Definition at line 428 of file SimParameters.h.

Referenced by getBondLambda().

Definition at line 411 of file SimParameters.h.

Referenced by ComputePmeUtil::select().

Definition at line 406 of file SimParameters.h.

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

Definition at line 387 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 393 of file SimParameters.h.

Definition at line 386 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 407 of file SimParameters.h.

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

Definition at line 422 of file SimParameters.h.

Referenced by getRepLambda(), and getVdwLambda().

Definition at line 388 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 417 of file SimParameters.h.

Referenced by getVdwLambda().

Definition at line 409 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 392 of file SimParameters.h.

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

Definition at line 988 of file SimParameters.h.

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

Definition at line 211 of file SimParameters.h.

Definition at line 682 of file SimParameters.h.

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

Definition at line 684 of file SimParameters.h.

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

Definition at line 683 of file SimParameters.h.

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

Definition at line 681 of file SimParameters.h.

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

Definition at line 228 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Definition at line 226 of file SimParameters.h.

Definition at line 1026 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1027 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1029 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1028 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

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 802 of file SimParameters.h.

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

Definition at line 127 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 128 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 129 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 130 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 582 of file SimParameters.h.

Definition at line 584 of file SimParameters.h.

Definition at line 585 of file SimParameters.h.

Definition at line 1035 of file SimParameters.h.

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

Definition at line 879 of file SimParameters.h.

Definition at line 880 of file SimParameters.h.

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

Definition at line 342 of file SimParameters.h.

Definition at line 340 of file SimParameters.h.

Definition at line 344 of file SimParameters.h.

Referenced by ComputeConsTorque::doForce().

Definition at line 343 of file SimParameters.h.

Definition at line 345 of file SimParameters.h.

Definition at line 263 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 291 of file SimParameters.h.

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

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 282 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 548 of file SimParameters.h.

Referenced by Parameters::Parameters().

Definition at line 849 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 854 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 855 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 856 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 857 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 852 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 853 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 846 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 850 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 851 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 848 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 974 of file SimParameters.h.

Definition at line 974 of file SimParameters.h.

Definition at line 974 of file SimParameters.h.

Definition at line 212 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 202 of file SimParameters.h.

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

Definition at line 204 of file SimParameters.h.

Referenced by Output::coordinate().

Definition at line 970 of file SimParameters.h.

Definition at line 970 of file SimParameters.h.

Definition at line 970 of file SimParameters.h.

Definition at line 581 of file SimParameters.h.

Definition at line 164 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

Definition at line 967 of file SimParameters.h.

Definition at line 967 of file SimParameters.h.

Definition at line 540 of file SimParameters.h.

Referenced by BondElem::computeForce(), and scriptSet().

Definition at line 536 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 541 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 535 of file SimParameters.h.

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

Definition at line 861 of file SimParameters.h.

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

Definition at line 862 of file SimParameters.h.

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

Definition at line 860 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Definition at line 859 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 863 of file SimParameters.h.

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

Definition at line 197 of file SimParameters.h.

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

Definition at line 459 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 460 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 458 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 457 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 875 of file SimParameters.h.

Definition at line 876 of file SimParameters.h.

Definition at line 817 of file SimParameters.h.

Definition at line 818 of file SimParameters.h.

Definition at line 819 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 141 of file SimParameters.h.

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

Definition at line 563 of file SimParameters.h.

Referenced by CollectionMgr::submitForces().

Definition at line 722 of file SimParameters.h.

Definition at line 721 of file SimParameters.h.

Definition at line 719 of file SimParameters.h.

Definition at line 720 of file SimParameters.h.

Definition at line 137 of file SimParameters.h.

Definition at line 766 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Definition at line 767 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Definition at line 214 of file SimParameters.h.

Definition at line 207 of file SimParameters.h.

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

Definition at line 557 of file SimParameters.h.

Referenced by ComputeMgr::createComputes(), and ParallelIOMgr::freeMolSpace().

Definition at line 520 of file SimParameters.h.

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

Definition at line 1010 of file SimParameters.h.

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

Definition at line 549 of file SimParameters.h.

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

Definition at line 580 of file SimParameters.h.

Definition at line 302 of file SimParameters.h.

Definition at line 301 of file SimParameters.h.

Definition at line 274 of file SimParameters.h.

Definition at line 269 of file SimParameters.h.

Definition at line 270 of file SimParameters.h.

Definition at line 271 of file SimParameters.h.

Definition at line 273 of file SimParameters.h.

Definition at line 266 of file SimParameters.h.

Definition at line 268 of file SimParameters.h.

Definition at line 272 of file SimParameters.h.

Definition at line 267 of file SimParameters.h.

Definition at line 993 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 967 of file SimParameters.h.

Definition at line 911 of file SimParameters.h.

Referenced by HomePatch::doGroupSizeCheck().

Definition at line 145 of file SimParameters.h.

Referenced by NamdHybridLB::NamdHybridLB().

Definition at line 957 of file SimParameters.h.

Definition at line 908 of file SimParameters.h.

Definition at line 978 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

Definition at line 524 of file SimParameters.h.

Definition at line 568 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 569 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 565 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 687 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

Definition at line 143 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

Definition at line 138 of file SimParameters.h.

Referenced by LdbCoordinator::createLoadBalancer().

Definition at line 146 of file SimParameters.h.

Definition at line 148 of file SimParameters.h.

Definition at line 140 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

Definition at line 147 of file SimParameters.h.

Definition at line 149 of file SimParameters.h.

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

Definition at line 139 of file SimParameters.h.

Referenced by NamdCentLB::Strategy().

Definition at line 181 of file SimParameters.h.

Definition at line 182 of file SimParameters.h.

Definition at line 179 of file SimParameters.h.

Definition at line 180 of file SimParameters.h.

Definition at line 441 of file SimParameters.h.

Definition at line 237 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 1037 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 119 of file SimParameters.h.

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

Definition at line 905 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 577 of file SimParameters.h.

Definition at line 574 of file SimParameters.h.

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

Definition at line 576 of file SimParameters.h.

Definition at line 575 of file SimParameters.h.

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

Definition at line 1014 of file SimParameters.h.

Referenced by Node::startup().

Definition at line 231 of file SimParameters.h.

Referenced by HomePatch::doMarginCheck().

Definition at line 247 of file SimParameters.h.

Definition at line 245 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 945 of file SimParameters.h.

Definition at line 831 of file SimParameters.h.

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

Definition at line 933 of file SimParameters.h.

Definition at line 178 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 931 of file SimParameters.h.

Definition at line 897 of file SimParameters.h.

Referenced by Controller::printEnergies().

Definition at line 1045 of file SimParameters.h.

Definition at line 1040 of file SimParameters.h.

Definition at line 1042 of file SimParameters.h.

Definition at line 1043 of file SimParameters.h.

Definition at line 1041 of file SimParameters.h.

Definition at line 1046 of file SimParameters.h.

Definition at line 1044 of file SimParameters.h.

Definition at line 943 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 828 of file SimParameters.h.

Definition at line 825 of file SimParameters.h.

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

Definition at line 830 of file SimParameters.h.

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

Definition at line 829 of file SimParameters.h.

Referenced by Controller::minimize().

Definition at line 827 of file SimParameters.h.

Definition at line 826 of file SimParameters.h.

Referenced by Controller::minimize().

Definition at line 558 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 915 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

Definition at line 914 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

Definition at line 322 of file SimParameters.h.

Definition at line 324 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

Definition at line 325 of file SimParameters.h.

Definition at line 308 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 310 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 734 of file SimParameters.h.

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

Definition at line 744 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 745 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 746 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 748 of file SimParameters.h.

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

Definition at line 740 of file SimParameters.h.

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

Definition at line 750 of file SimParameters.h.

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

Definition at line 730 of file SimParameters.h.

Definition at line 763 of file SimParameters.h.

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

Definition at line 757 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 756 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 759 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 758 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 761 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 760 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 902 of file SimParameters.h.

Referenced by Sequencer::integrate().

Definition at line 698 of file SimParameters.h.

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

Definition at line 133 of file SimParameters.h.

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

Definition at line 185 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 184 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 183 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 939 of file SimParameters.h.

Definition at line 941 of file SimParameters.h.

Definition at line 935 of file SimParameters.h.

Definition at line 937 of file SimParameters.h.

Definition at line 1025 of file SimParameters.h.

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

Definition at line 1033 of file SimParameters.h.

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

Definition at line 152 of file SimParameters.h.

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

Definition at line 891 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::finishReductions().

Definition at line 160 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

Definition at line 885 of file SimParameters.h.

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

Definition at line 259 of file SimParameters.h.

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

Definition at line 947 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Definition at line 894 of file SimParameters.h.

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

Definition at line 888 of file SimParameters.h.

Referenced by Controller::printTiming().

Definition at line 544 of file SimParameters.h.

Definition at line 545 of file SimParameters.h.

Definition at line 249 of file SimParameters.h.

Definition at line 257 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Definition at line 251 of file SimParameters.h.

Definition at line 256 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Definition at line 255 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects().

Definition at line 258 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Definition at line 780 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 771 of file SimParameters.h.

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

Definition at line 776 of file SimParameters.h.

Definition at line 779 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 778 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 781 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 782 of file SimParameters.h.

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

Definition at line 786 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 783 of file SimParameters.h.

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

Definition at line 785 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 784 of file SimParameters.h.

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

Definition at line 777 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 787 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize_pencils().

Definition at line 770 of file SimParameters.h.

Definition at line 708 of file SimParameters.h.

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

Definition at line 709 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 710 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 711 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 706 of file SimParameters.h.

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

Definition at line 515 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Definition at line 1015 of file SimParameters.h.

Definition at line 1019 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

Definition at line 1018 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

Definition at line 1021 of file SimParameters.h.

Referenced by Node::startup().

Definition at line 473 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 483 of file SimParameters.h.

Definition at line 484 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 482 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 488 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 487 of file SimParameters.h.

Definition at line 485 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

Definition at line 486 of file SimParameters.h.

Definition at line 467 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 471 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 470 of file SimParameters.h.

Definition at line 472 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 508 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 509 of file SimParameters.h.

Definition at line 498 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 511 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

Definition at line 468 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 478 of file SimParameters.h.

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

Definition at line 503 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 506 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 505 of file SimParameters.h.

Definition at line 504 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 480 of file SimParameters.h.

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

Definition at line 497 of file SimParameters.h.

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

Definition at line 512 of file SimParameters.h.

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

Definition at line 465 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 466 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 493 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 492 of file SimParameters.h.

Definition at line 499 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 489 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 491 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 490 of file SimParameters.h.

Definition at line 513 of file SimParameters.h.

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

Definition at line 476 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 477 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 479 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 474 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 475 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 494 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

Definition at line 469 of file SimParameters.h.

Definition at line 496 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 989 of file SimParameters.h.

Referenced by buildExclusions().

Definition at line 949 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 224 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Definition at line 225 of file SimParameters.h.

Definition at line 315 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 316 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 313 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 317 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 332 of file SimParameters.h.

Definition at line 330 of file SimParameters.h.

Definition at line 334 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

Definition at line 333 of file SimParameters.h.

Definition at line 335 of file SimParameters.h.

Definition at line 199 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 1000 of file SimParameters.h.

Referenced by HomePatch::exchangeAtoms(), and scriptSet().

Definition at line 1001 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 1002 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 1003 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 1005 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 1007 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 280 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 163 of file SimParameters.h.

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

Definition at line 352 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 355 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 353 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 354 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 350 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 356 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 351 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

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

Definition at line 455 of file SimParameters.h.

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

scaling factor for solute interactions

Definition at line 447 of file SimParameters.h.

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

optional independent control over scaling factor for electrostatic interactions of solute

Definition at line 449 of file SimParameters.h.

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

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

Definition at line 452 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 843 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 844 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 837 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 839 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 834 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 841 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 842 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 836 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 288 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

Definition at line 289 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

Definition at line 910 of file SimParameters.h.

Definition at line 928 of file SimParameters.h.

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

Definition at line 871 of file SimParameters.h.

Referenced by ComputeStir::ComputeStir(), and scriptSet().

Definition at line 866 of file SimParameters.h.

Definition at line 870 of file SimParameters.h.

Referenced by ComputeStir::doForce().

Definition at line 872 of file SimParameters.h.

Referenced by ComputeStir::ComputeStir(), and scriptSet().

Definition at line 868 of file SimParameters.h.

Definition at line 869 of file SimParameters.h.

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 605 of file SimParameters.h.

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

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

Definition at line 608 of file SimParameters.h.

Referenced by Controller::printEnergies().

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 592 of file SimParameters.h.

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

Timescale (ps) for stochastic velocity rescaling.

Definition at line 602 of file SimParameters.h.

Referenced by Controller::Controller().

Temperature for stochastic velocity rescaling.

Definition at line 599 of file SimParameters.h.

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

Definition at line 1036 of file SimParameters.h.

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

Definition at line 713 of file SimParameters.h.

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

Definition at line 714 of file SimParameters.h.

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

Definition at line 531 of file SimParameters.h.

Referenced by ComputeLCPO::ComputeLCPO().

Definition at line 380 of file SimParameters.h.

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 378 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 379 of file SimParameters.h.

Definition at line 382 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 381 of file SimParameters.h.

Definition at line 377 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 377 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 363 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 365 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 361 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 364 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 360 of file SimParameters.h.

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

Definition at line 362 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 556 of file SimParameters.h.

Referenced by ComputeTclBC::doWork(), and scriptSet().

Definition at line 554 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 552 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Definition at line 926 of file SimParameters.h.

Definition at line 369 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 374 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 373 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 374 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 370 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 373 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 369 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 372 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 930 of file SimParameters.h.

Definition at line 151 of file SimParameters.h.

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

Definition at line 175 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 176 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 177 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 960 of file SimParameters.h.

Definition at line 1009 of file SimParameters.h.

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

Definition at line 672 of file SimParameters.h.

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

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

Definition at line 797 of file SimParameters.h.

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

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 808 of file SimParameters.h.

Definition at line 790 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 253 of file SimParameters.h.

Definition at line 1012 of file SimParameters.h.

Referenced by NamdState::loadStructure().

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

Definition at line 793 of file SimParameters.h.

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

Definition at line 241 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 996 of file SimParameters.h.

Definition at line 990 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 213 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 205 of file SimParameters.h.

Referenced by Output::velocity(), and Output::velocityNeeded().

Definition at line 165 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

Definition at line 195 of file SimParameters.h.

Referenced by ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int().

Definition at line 215 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Definition at line 209 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Definition at line 191 of file SimParameters.h.

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

Definition at line 192 of file SimParameters.h.

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


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

Generated on 6 Dec 2019 for NAMD by  doxygen 1.6.1