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 singleTopology
Bool sdScaling
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
Bool useAVXTiles

Detailed Description

Definition at line 100 of file SimParameters.h.


Constructor & Destructor Documentation

SimParameters::SimParameters (  )  [inline]

Definition at line 1055 of file SimParameters.h.

01055 : mgridforcelist(), parseopts(0) {};

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

Definition at line 1056 of file SimParameters.h.

References initialize_config_data().

01056                                                  : mgridforcelist(), parseopts(0) {
01057           initialize_config_data(c,cwd);
01058         };

SimParameters::~SimParameters (  )  [inline]

Definition at line 1059 of file SimParameters.h.

01059 {};


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 7246 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().

07246                                                          {
07247   // Convenience function for staggered lambda scaling
07248   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
07249 }

BigReal SimParameters::getCurrentLambda ( const int  step  ) 

Definition at line 7167 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().

07167                                                       {
07168   /*Get lambda at the current step. 
07169 
07170    If alchLambdaFreq = 0, return alchLambda. For positive values of 
07171    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
07172    alchLambda2:
07173 
07174    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
07175 
07176    n - the current time step
07177    n0 - step at which switching begins (default = 0)
07178    N - total steps in the simulation
07179    dn - alchLambdaFreq (increment frequency, in steps)
07180    l/l2 - alchLambda/alchLambda2
07181  
07182    Note that each step _begins_ by incrementing alchLambda and then integrates
07183    in time. This means that the first and last switch steps may not behave as
07184    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
07185    no step occurs because alchLambda2 has already been reached.
07186   */
07187   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
07188     if ( step == N ) {
07189       return alchLambda2;
07190     }
07191     else {
07192       const int timeOrigin = firstTimestep + alchEquilSteps;
07193       const BigReal alchLambdaDelta = getLambdaDelta();
07194       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
07195       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
07196     }
07197   }
07198   else {
07199     return alchLambda;
07200   }
07201 }

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

Definition at line 7209 of file SimParameters.C.

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

07209                                                          {
07210   // Convenience function for staggered lambda scaling
07211   return (lambda <= alchElecLambdaStart ? 0.
07212           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
07213 }

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

Definition at line 104 of file SimParameters.C.

References ParseOptions::getfromptr().

00104                                                                     {
00105   if ( parseopts ) return parseopts->getfromptr(name,outbuf);
00106   else return 0;
00107 }

BigReal SimParameters::getLambdaDelta ( void   ) 

Definition at line 7203 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, and firstTimestep.

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

07203                                           {
07204   // Increment by which Lambda changes.
07205   return ((alchLambda2 - alchLambda)*alchLambdaFreq
07206           / BigReal(N - firstTimestep - alchEquilSteps));
07207 }

BigReal SimParameters::getRepLambda ( const BigReal  lambda  ) 

Definition at line 7241 of file SimParameters.C.

References alchRepLambdaEnd.

07241                                                         {
07242   // Convenience function for staggered lambda scaling
07243   return (lambda >= alchRepLambdaEnd ? 1. : lambda / alchRepLambdaEnd);
07244 }

BigReal SimParameters::getVdwLambda ( const BigReal  lambda  ) 

Definition at line 7223 of file SimParameters.C.

References alchRepLambdaEnd, alchVdwLambdaEnd, and alchWCAOn.

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

07223                                                         {
07224   // Convenience function for staggered lambda scaling
07225   if ( alchWCAOn ) {
07226     // Read this with the alias alchRepLambdaEnd --> alchAttLambdaStart.
07227     // The second condition is needed when attractive interactions are inactive
07228     // for the whole range, otherwise lambda = 0/1 are incorrect.
07229     if ( lambda < alchRepLambdaEnd || alchRepLambdaEnd == 1.0 ) {
07230       return 0.0;
07231     } else if ( lambda >= alchVdwLambdaEnd ) {
07232       return 1.0;
07233     } else {
07234       return (lambda - alchRepLambdaEnd) / (alchVdwLambdaEnd - alchRepLambdaEnd);
07235     }
07236   } else {
07237     return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
07238   }
07239 }

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

Definition at line 132 of file SimParameters.C.

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

Referenced by SimParameters().

00134 {
00135 
00136    parseopts = new ParseOptions;   //  Object to check consistency of config file
00137    ParseOptions &opts = *parseopts;
00138 
00139    config_parser(opts);
00140 
00142    if (!opts.check_consistency()) 
00143    {
00144       NAMD_die("Internal error in configuration file parser");
00145    }
00146 
00147    // Now, feed the object with the actual configuration options through the
00148    // ParseOptions file and make sure everything is OK
00149    if (!opts.set(*config)) 
00150    {
00151       NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00152    }
00153 
00155 
00156    check_config(opts,config,cwd);
00157 
00158    print_config(opts,config,cwd);
00159 
00160 }

int SimParameters::isRecvSpanningTreeOn (  )  [inline]

Definition at line 1081 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

01081 { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (  )  [inline]

Definition at line 1082 of file SimParameters.h.

References proxyRecvSpanningTree.

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

01082 { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (  )  [inline]

Definition at line 1079 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

01079 { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (  )  [inline]

Definition at line 1080 of file SimParameters.h.

References proxySendSpanningTree.

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

01080 { return proxySendSpanningTree == -1; }

int SimParameters::issetinparseopts ( const char *  name  ) 

Definition at line 114 of file SimParameters.C.

References ParseOptions::issetfromptr().

00114                                                     {
00115   if ( parseopts ) return parseopts->issetfromptr(name);
00116   else return -1;
00117 }

int SimParameters::istrueinparseopts ( const char *  name  ) 

Definition at line 109 of file SimParameters.C.

References ParseOptions::istruefromptr().

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

void SimParameters::nonbonded_select (  )  [static]

Definition at line 397 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

00397                                      {
00398     ComputeNonbondedUtil::select();
00399 }

void SimParameters::pme_select (  )  [static]

Definition at line 401 of file SimParameters.C.

References ComputePmeUtil::select().

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

00401                                {
00402   ComputePmeUtil::select();
00403 }

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

Definition at line 2330 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.

02330                                                                             {
02331 
02332      if ( ! latptr ) {
02333        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
02334      }
02335 
02336      ifstream xscFile(filename);
02337      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
02338 
02339      char labels[1024];
02340      do {
02341        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02342        xscFile.getline(labels,1023);
02343      } while ( strncmp(labels,"#$LABELS ",9) );
02344 
02345      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
02346      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
02347      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
02348      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
02349 
02350      int pos = 0;
02351      char *l_i = labels + 8;
02352      while ( *l_i ) {
02353        if ( *l_i == ' ' ) { ++l_i; continue; }
02354        char *l_i2;
02355        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
02356        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
02357          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
02358          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
02359          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
02360          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
02361          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
02362          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
02363          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
02364          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
02365          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
02366          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
02367          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
02368          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
02369          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
02370          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
02371          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
02372          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
02373          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
02374          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
02375        }
02376        ++pos;
02377        l_i = l_i2;
02378      }
02379      int numpos = pos;
02380 
02381      for ( pos = 0; pos < numpos; ++pos ) {
02382        double tmp;
02383        xscFile >> tmp;
02384        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02385        if ( pos == a_x ) cellBasisVector1.x = tmp;
02386        if ( pos == a_y ) cellBasisVector1.y = tmp;
02387        if ( pos == a_z ) cellBasisVector1.z = tmp;
02388        if ( pos == b_x ) cellBasisVector2.x = tmp;
02389        if ( pos == b_y ) cellBasisVector2.y = tmp;
02390        if ( pos == b_z ) cellBasisVector2.z = tmp;
02391        if ( pos == c_x ) cellBasisVector3.x = tmp;
02392        if ( pos == c_y ) cellBasisVector3.y = tmp;
02393        if ( pos == c_z ) cellBasisVector3.z = tmp;
02394        if ( pos == o_x ) cellOrigin.x = tmp;
02395        if ( pos == o_y ) cellOrigin.y = tmp;
02396        if ( pos == o_z ) cellOrigin.z = tmp;
02397        if ( pos == s_u ) strainRate2.x = tmp;
02398        if ( pos == s_v ) strainRate2.y = tmp;
02399        if ( pos == s_w ) strainRate2.z = tmp;
02400        if ( pos == s_x ) strainRate.x = tmp;
02401        if ( pos == s_y ) strainRate.y = tmp;
02402        if ( pos == s_z ) strainRate.z = tmp;
02403      }
02404 
02405    if ( latptr ) {
02406      Lattice test;
02407      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02408     
02409      if ( test.a_p() && ! lattice.a_p() ) {
02410        NAMD_die("cellBasisVector1 added during atom reinitialization");
02411      }
02412      if ( lattice.a_p() && ! test.a_p() ) {
02413        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
02414      }
02415      if ( test.b_p() && ! lattice.b_p() ) {
02416        NAMD_die("cellBasisVector2 added during atom reinitialization");
02417      }
02418      if ( lattice.b_p() && ! test.b_p() ) {
02419        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
02420      }
02421      if ( test.c_p() && ! lattice.c_p() ) {
02422        NAMD_die("cellBasisVector3 added during atom reinitialization");
02423      }
02424      if ( lattice.c_p() && ! test.c_p() ) {
02425        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
02426      }
02427 
02428      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02429    }
02430 
02431 }

void SimParameters::receive_SimParameters ( MIStream msg  ) 

Definition at line 7070 of file SimParameters.C.

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

07072 {
07073   msg->get(sizeof(SimParameters),(char*)this);
07074   if ( FFTWWisdomString ) {
07075     int fftwlen;
07076     msg->get(fftwlen);
07077     FFTWWisdomString = new char[fftwlen];
07078     msg->get(fftwlen,FFTWWisdomString);
07079 #ifdef NAMD_FFTW
07080 #ifdef NAMD_FFTW_3
07081     fftwf_import_wisdom_from_string(FFTWWisdomString);
07082 #else
07083     fftw_import_wisdom_from_string(FFTWWisdomString);
07084 #endif
07085 #endif
07086   }
07087   if ( tclBCScript ) {
07088     int tcllen;
07089     msg->get(tcllen);
07090     tclBCScript = new char[tcllen];
07091     msg->get(tcllen,tclBCScript);
07092   }
07093 
07094 #ifdef MEM_OPT_VERSION
07095   int filelen;
07096   msg->get(filelen);
07097   binAtomFile = new char[filelen];
07098   msg->get(filelen, binAtomFile);
07099   
07100   msg->get(filelen);
07101   binCoorFile = new char[filelen];
07102   msg->get(filelen, binCoorFile);
07103 
07104   if(binVelFile) {    
07105     msg->get(filelen);
07106     binVelFile = new char[filelen];
07107     msg->get(filelen, binVelFile);
07108   }
07109 
07110   if(binRefFile) {    
07111     msg->get(filelen);
07112     binRefFile = new char[filelen];
07113     msg->get(filelen, binRefFile);
07114   }
07115 #endif
07116 
07117 
07118   // The simParameters bit copy above put illegal values in the list pointers
07119   // So this resets everything so that unpacking will work.
07120   mgridforcelist.clear();
07121   mgridforcelist.unpack_data(msg);
07122   
07123   delete msg;
07124 }

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

Definition at line 174 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().

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

void SimParameters::send_SimParameters ( MOStream msg  ) 

Definition at line 7012 of file SimParameters.C.

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

07014 {
07015   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
07016   if ( msg == NULL )
07017   {
07018     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
07019   }*/
07020 
07021   msg->put(sizeof(SimParameters),(char*)this);
07022   if ( FFTWWisdomString ) {
07023     int fftwlen = strlen(FFTWWisdomString) + 1;
07024     msg->put(fftwlen);
07025     msg->put(fftwlen,FFTWWisdomString);
07026   }
07027   if ( tclBCScript ) {
07028     int tcllen = strlen(tclBCScript) + 1;
07029     msg->put(tcllen);
07030     msg->put(tcllen,tclBCScript);
07031   }
07032 
07033 #ifdef MEM_OPT_VERSION
07034   int filelen = strlen(binAtomFile)+1;
07035   msg->put(filelen);
07036   msg->put(filelen, binAtomFile);
07037 
07038   filelen = strlen(binCoorFile)+1;
07039   msg->put(filelen);
07040   msg->put(filelen, binCoorFile);
07041 
07042   if(binVelFile) {
07043     filelen = strlen(binVelFile)+1;
07044     msg->put(filelen);
07045     msg->put(filelen, binVelFile);
07046   }
07047 
07048   if(binRefFile) {
07049     filelen = strlen(binRefFile)+1;
07050     msg->put(filelen);
07051     msg->put(filelen, binRefFile);
07052   }
07053 #endif
07054 
07055   mgridforcelist.pack_data(msg);
07056   
07057   msg->end();
07058 }

int SimParameters::setupIDWS (  ) 

Definition at line 7139 of file SimParameters.C.

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

Referenced by scriptSet().

07139                              {
07140   if (alchLambdaIDWS < 0.) return 0;
07141   if (alchLambdaIDWS > 1.) {
07142     NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
07143   }
07144  /* 
07145   * The internal parameter alchIDWSFreq determines the number of steps of MD
07146   * before each switch of the value of alchLambda2. At most this occurs every
07147   * time the energy is evaluated and thus the default is the greater of
07148   * fullElectFrequency and nonbondedFrequency. However, this choice fails to
07149   * report alternating values if output is printed less often than every step
07150   * (which is almost certainly true). Thus the frequency is reset to match
07151   * alchOutFreq or, if that is zero, outputEnergies. Note that, if 
07152   * alchOutFreq > 0 but != outputEnergies, then the data going to stdout
07153   * are likely not useful since the comparison value is difficult to infer.
07154   */
07155   alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency;
07156   if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies;
07157   if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq;
07158   if ( alchOutFreq && alchOutFreq != outputEnergies) {
07159     iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput"
07160          << " to stdout may not be useful!\n" << endi;
07161   }
07162   return 1;
07163 }


Member Data Documentation

Definition at line 969 of file SimParameters.h.

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 621 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 629 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 633 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 631 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 634 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 640 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 638 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 639 of file SimParameters.h.

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

Definition at line 637 of file SimParameters.h.

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

Definition at line 636 of file SimParameters.h.

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

Definition at line 635 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 622 of file SimParameters.h.

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

Definition at line 623 of file SimParameters.h.

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

Definition at line 627 of file SimParameters.h.

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

Definition at line 626 of file SimParameters.h.

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

Definition at line 651 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 652 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 654 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 644 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 653 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 645 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

Definition at line 648 of file SimParameters.h.

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

Definition at line 657 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 647 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 660 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 656 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

Definition at line 658 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 650 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 649 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 436 of file SimParameters.h.

Referenced by CrosstermElem::computeForce().

Definition at line 430 of file SimParameters.h.

Referenced by getBondLambda().

Definition at line 413 of file SimParameters.h.

Referenced by ComputePmeUtil::select().

Definition at line 408 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 395 of file SimParameters.h.

Definition at line 386 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 409 of file SimParameters.h.

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

Definition at line 424 of file SimParameters.h.

Referenced by getRepLambda(), and getVdwLambda().

Definition at line 388 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 419 of file SimParameters.h.

Referenced by getVdwLambda().

Definition at line 411 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 394 of file SimParameters.h.

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

Definition at line 990 of file SimParameters.h.

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

Definition at line 211 of file SimParameters.h.

Definition at line 684 of file SimParameters.h.

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

Definition at line 686 of file SimParameters.h.

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

Definition at line 685 of file SimParameters.h.

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

Definition at line 683 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 1028 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 1031 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1030 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 804 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 584 of file SimParameters.h.

Definition at line 586 of file SimParameters.h.

Definition at line 587 of file SimParameters.h.

Definition at line 1037 of file SimParameters.h.

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

Definition at line 881 of file SimParameters.h.

Definition at line 882 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 550 of file SimParameters.h.

Referenced by Parameters::Parameters().

Definition at line 851 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 858 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 859 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 848 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

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 850 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 976 of file SimParameters.h.

Definition at line 976 of file SimParameters.h.

Definition at line 976 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 972 of file SimParameters.h.

Definition at line 972 of file SimParameters.h.

Definition at line 972 of file SimParameters.h.

Definition at line 583 of file SimParameters.h.

Definition at line 164 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

Definition at line 969 of file SimParameters.h.

Definition at line 969 of file SimParameters.h.

Definition at line 542 of file SimParameters.h.

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

Definition at line 538 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 543 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 537 of file SimParameters.h.

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

Definition at line 863 of file SimParameters.h.

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

Definition at line 864 of file SimParameters.h.

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

Definition at line 862 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Definition at line 861 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 865 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 461 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 462 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 460 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 459 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 877 of file SimParameters.h.

Definition at line 878 of file SimParameters.h.

Definition at line 819 of file SimParameters.h.

Definition at line 820 of file SimParameters.h.

Definition at line 821 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 565 of file SimParameters.h.

Referenced by CollectionMgr::submitForces().

Definition at line 724 of file SimParameters.h.

Definition at line 723 of file SimParameters.h.

Definition at line 721 of file SimParameters.h.

Definition at line 722 of file SimParameters.h.

Definition at line 137 of file SimParameters.h.

Definition at line 768 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Definition at line 769 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 559 of file SimParameters.h.

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

Definition at line 522 of file SimParameters.h.

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

Definition at line 1012 of file SimParameters.h.

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

Definition at line 551 of file SimParameters.h.

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

Definition at line 582 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 995 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 969 of file SimParameters.h.

Definition at line 913 of file SimParameters.h.

Referenced by HomePatch::doGroupSizeCheck().

Definition at line 145 of file SimParameters.h.

Referenced by NamdHybridLB::NamdHybridLB().

Definition at line 959 of file SimParameters.h.

Definition at line 910 of file SimParameters.h.

Definition at line 980 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

Definition at line 526 of file SimParameters.h.

Definition at line 570 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 571 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 567 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 689 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 443 of file SimParameters.h.

Definition at line 237 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 1039 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 907 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 579 of file SimParameters.h.

Definition at line 576 of file SimParameters.h.

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

Definition at line 578 of file SimParameters.h.

Definition at line 577 of file SimParameters.h.

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

Definition at line 1016 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 947 of file SimParameters.h.

Definition at line 833 of file SimParameters.h.

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

Definition at line 935 of file SimParameters.h.

Definition at line 178 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 933 of file SimParameters.h.

Definition at line 899 of file SimParameters.h.

Referenced by Controller::printEnergies().

Definition at line 1047 of file SimParameters.h.

Definition at line 1042 of file SimParameters.h.

Definition at line 1044 of file SimParameters.h.

Definition at line 1045 of file SimParameters.h.

Definition at line 1043 of file SimParameters.h.

Definition at line 1048 of file SimParameters.h.

Definition at line 1046 of file SimParameters.h.

Definition at line 945 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 830 of file SimParameters.h.

Definition at line 827 of file SimParameters.h.

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

Definition at line 832 of file SimParameters.h.

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

Definition at line 831 of file SimParameters.h.

Referenced by Controller::minimize().

Definition at line 829 of file SimParameters.h.

Definition at line 828 of file SimParameters.h.

Referenced by Controller::minimize().

Definition at line 560 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 917 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

Definition at line 916 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 736 of file SimParameters.h.

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

Definition at line 746 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 747 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 748 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 750 of file SimParameters.h.

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

Definition at line 742 of file SimParameters.h.

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

Definition at line 752 of file SimParameters.h.

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

Definition at line 732 of file SimParameters.h.

Definition at line 765 of file SimParameters.h.

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

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 763 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 762 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 904 of file SimParameters.h.

Referenced by Sequencer::integrate().

Definition at line 700 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 941 of file SimParameters.h.

Definition at line 943 of file SimParameters.h.

Definition at line 937 of file SimParameters.h.

Definition at line 939 of file SimParameters.h.

Definition at line 1027 of file SimParameters.h.

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

Definition at line 1035 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 893 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::finishReductions().

Definition at line 160 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

Definition at line 887 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 949 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Definition at line 896 of file SimParameters.h.

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

Definition at line 890 of file SimParameters.h.

Referenced by Controller::printTiming().

Definition at line 546 of file SimParameters.h.

Definition at line 547 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 782 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 773 of file SimParameters.h.

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

Definition at line 778 of file SimParameters.h.

Definition at line 781 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 780 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 783 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 788 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 785 of file SimParameters.h.

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

Definition at line 787 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 786 of file SimParameters.h.

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

Definition at line 779 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 789 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize_pencils().

Definition at line 772 of file SimParameters.h.

Definition at line 710 of file SimParameters.h.

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

Definition at line 711 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 712 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 713 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 708 of file SimParameters.h.

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

Definition at line 517 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Definition at line 1017 of file SimParameters.h.

Definition at line 1021 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

Definition at line 1020 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

Definition at line 1023 of file SimParameters.h.

Referenced by Node::startup().

Definition at line 475 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 485 of file SimParameters.h.

Definition at line 486 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 484 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 490 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 489 of file SimParameters.h.

Definition at line 487 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

Definition at line 488 of file SimParameters.h.

Definition at line 469 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 473 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 472 of file SimParameters.h.

Definition at line 474 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 510 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 511 of file SimParameters.h.

Definition at line 500 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 513 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

Definition at line 470 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 480 of file SimParameters.h.

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

Definition at line 505 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 507 of file SimParameters.h.

Definition at line 506 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 482 of file SimParameters.h.

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

Definition at line 499 of file SimParameters.h.

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

Definition at line 514 of file SimParameters.h.

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

Definition at line 467 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 468 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 495 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 494 of file SimParameters.h.

Definition at line 501 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 491 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 493 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 492 of file SimParameters.h.

Definition at line 515 of file SimParameters.h.

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

Definition at line 478 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 479 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 481 of file SimParameters.h.

Referenced by NamdState::loadStructure().

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 496 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

Definition at line 471 of file SimParameters.h.

Definition at line 498 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 991 of file SimParameters.h.

Referenced by buildExclusions().

Definition at line 951 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 1002 of file SimParameters.h.

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

Definition at line 1003 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 1004 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 1009 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 457 of file SimParameters.h.

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

scaling factor for solute interactions

Definition at line 449 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 451 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 454 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 845 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 846 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 839 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 841 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 836 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

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 838 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 912 of file SimParameters.h.

Definition at line 930 of file SimParameters.h.

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

Definition at line 873 of file SimParameters.h.

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

Definition at line 868 of file SimParameters.h.

Definition at line 872 of file SimParameters.h.

Referenced by ComputeStir::doForce().

Definition at line 874 of file SimParameters.h.

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

Definition at line 870 of file SimParameters.h.

Definition at line 871 of file SimParameters.h.

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 607 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 610 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 594 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 604 of file SimParameters.h.

Referenced by Controller::Controller().

Temperature for stochastic velocity rescaling.

Definition at line 601 of file SimParameters.h.

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

Definition at line 1038 of file SimParameters.h.

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

Definition at line 715 of file SimParameters.h.

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

Definition at line 716 of file SimParameters.h.

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

Definition at line 533 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 558 of file SimParameters.h.

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

Definition at line 556 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 554 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Definition at line 928 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 932 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 962 of file SimParameters.h.

Definition at line 1011 of file SimParameters.h.

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

Definition at line 674 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 799 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 810 of file SimParameters.h.

Definition at line 792 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 253 of file SimParameters.h.

Definition at line 1014 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 795 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 998 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 992 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 21 Sep 2020 for NAMD by  doxygen 1.6.1