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

Static Public Member Functions

static void nonbonded_select ()
static void pme_select ()

Public Attributes

Bool lonepairs
int watmodel
Bool LJcorrection
BigReal dt
int N
int stepsPerCycle
zVector cellBasisVector1
zVector cellBasisVector2
zVector cellBasisVector3
zVector cellOrigin
Lattice lattice
int nonbondedFrequency
int fullElectFrequency
BigReal fmaTheta
int ldBalancer
int ldbStrategy
int ldbPeriod
int firstLdbStep
int lastLdbStep
int hybridGroupSize
BigReal ldbBackgroundScaling
BigReal ldbPMEBackgroundScaling
BigReal ldbHomeBackgroundScaling
BigReal ldbRelativeGrainsize
int traceStartStep
int numTraceSteps
Bool outputMaps
Bool simulateInitialMapping
int simulatedPEs
int simulatedNodeSize
Bool disableTopology
Bool verboseTopology
Bool benchTimestep
int useCkLoop
int twoAwayX
int twoAwayY
int twoAwayZ
int maxPatches
Bool ldbUnloadPME
Bool ldbUnloadZero
Bool ldbUnloadOne
Bool ldbUnloadOutputPEs
Bool noPatchesOnZero
Bool noPatchesOnOutputPEs
Bool noPatchesOnOne
BigReal initialTemp
Bool comMove
Bool zeroMomentum
Bool zeroMomentumAlt
Bool wrapWater
Bool wrapAll
Bool wrapNearest
BigReal dielectric
ExclusionSettings exclude
BigReal scale14
BigReal nonbondedScaling
int dcdFrequency
int dcdUnitCell
int velDcdFrequency
int forceDcdFrequency
int xstFrequency
char auxFilename [128]
char dcdFilename [128]
char velDcdFilename [128]
char forceDcdFilename [128]
char xstFilename [128]
char outputFilename [128]
char restartFilename [128]
int restartFrequency
Bool restartSave
Bool restartSaveDcd
Bool binaryRestart
Bool binaryOutput
BigReal cutoff
BigReal margin
BigReal patchDimension
BigReal limitDist
Bool switchingActive
Bool vdwForceSwitching
BigReal switchingDist
Bool martiniSwitching
Bool martiniDielAllow
BigReal pairlistDist
int pairlistMinProcs
int usePairlists
int pairlistsPerCycle
BigReal pairlistShrink
BigReal pairlistGrow
BigReal pairlistTrigger
int outputPairlists
Bool constraintsOn
int constraintExp
Bool gridforceOn
Bool gridforceVolts
zVector gridforceScale
Bool gridforceContA1
Bool gridforceContA2
Bool gridforceContA3
zVector gridforceVOffset
Bool gridforceLite
Bool gridforcechecksize
Bool mgridforceOn
MGridforceParamsList mgridforcelist
Bool selectConstraintsOn
Bool constrXOn
Bool constrYOn
Bool constrZOn
Bool sphericalConstraintsOn
zVector sphericalConstrCenter
BigReal constraintScaling
Bool paraTypeXplorOn
Bool paraTypeCharmmOn
Bool goGroPair
Bool goForcesOn
char goParameters [128]
char goCoordinates [128]
GoChoices goMethod
Bool movingConstraintsOn
zVector movingConsVel
Bool rotConstraintsOn
zVector rotConsAxis
zVector rotConsPivot
BigReal rotConsVel
Bool movDragOn
char movDragFile [128]
BigReal movDragGlobVel
char movDragVelFile [128]
Bool rotDragOn
char rotDragFile [128]
char rotDragAxisFile [128]
char rotDragPivotFile [128]
BigReal rotDragGlobVel
char rotDragVelFile [128]
Bool consTorqueOn
char consTorqueFile [128]
char consTorqueAxisFile [128]
char consTorquePivotFile [128]
BigReal consTorqueGlobVal
char consTorqueValFile [128]
Bool SMDOn
BigReal SMDVel
zVector SMDDir
BigReal SMDk
BigReal SMDk2
char SMDFile [128]
int SMDOutputFreq
Bool tabulatedEnergies
int tableNumTypes
char tabulatedEnergiesFile [128]
char tableInterpType [128]
Real tableSpacing
BigReal tableMaxDist
Bool TMDOn
Bool TMDDiffRMSD
BigReal TMDk
char TMDFile [128]
char TMDFile2 [128]
int TMDOutputFreq
int TMDFirstStep
int TMDLastStep
BigReal TMDInitialRMSD
BigReal TMDFinalRMSD
Bool symmetryOn
Bool symmetryScaleForces
BigReal symmetryk
char symmetrykfile [128]
char symmetryFile [128]
char symmetryMatrixFile [128]
int symmetryFirstStep
int symmetryLastStep
int symmetryFirstFullStep
int symmetryLastFullStep
Bool alchOnAtStartup
Bool alchFepOnAtStartup
Bool alchThermIntOnAtStartup
Bool alchOn
Bool alchFepOn
Bool alchThermIntOn
Bool alchFepWCARepuOn
Bool alchFepWCADispOn
Bool alchFepElecOn
Bool alchFepWhamOn
int alchMethod
BigReal alchLambda
BigReal alchLambda2
BigReal alchLambdaIDWS
int alchIDWSFreq
int alchLambdaFreq
BigReal alchRepLambda
BigReal alchDispLambda
BigReal alchElecLambda
BigReal alchFepWCArcut1
BigReal alchFepWCArcut2
BigReal alchFepWCArcut3
BigReal alchTemp
int alchOutFreq
Bool alchEnsembleAvg
char alchOutFile [128]
int alchEquilSteps
BigReal alchVdwShiftCoeff
BigReal alchElecLambdaStart
BigReal alchVdwLambdaEnd
BigReal alchBondLambdaEnd
Bool alchDecouple
Bool alchBondDecouple
Bool lesOn
int lesFactor
Bool lesReduceTemp
Bool lesReduceMass
Bool soluteScalingOn
BigReal soluteScalingFactor
BigReal soluteScalingFactorCharge
BigReal soluteScalingFactorVdw
Bool soluteScalingAll
Bool extForcesOn
char extForcesCommand [256]
char extCoordFilename [128]
char extForceFilename [128]
Bool qmForcesOn
char qmParamPDB [128]
Bool qmParamPDBDefined
Bool qmChrgFromPSF
char qmExecPath [256]
char qmSoftware [128]
char qmChrgModeS [16]
int qmChrgMode
char qmColumn [16]
char qmBaseDir [256]
char qmSecProc [256]
Bool qmSecProcOn
char qmPrepProc [256]
Bool qmPrepProcOn
int qmFormat
Bool qmReplaceAll
Bool qmMOPACAddConfigChrg
Bool qmBondOn
char qmBondColumn [16]
Bool qmBondDist
int qmBondValType
char qmBondValueTypeS [16]
char qmBondSchemeS [16]
int qmBondScheme
Bool qmPCSwitchOn
char qmPCSwitchTypeS [16]
int qmPCSwitchType
char qmPCSchemeS [16]
int qmPCScheme
int qmSimsPerNode
Bool qmVDW
Bool qmNoPC
Bool qmElecEmbed
int qmPCSelFreq
Bool qmCustomPCSel
Bool qmLSSOn
int qmLSSFreq
char qmLSSResname [5]
char qmLSSModeS [16]
int qmLSSMode
Bool qmCSMD
char qmCSMDFile [128]
int qmEnergyOutFreq
int qmOutFreq
int qmPosOutFreq
Bool printBadContacts
Bool GBISOn
BigReal fsMax
Bool GBISserOn
BigReal solvent_dielectric
BigReal coulomb_radius_offset
BigReal kappa
BigReal ion_concentration
BigReal gbis_delta
BigReal gbis_beta
BigReal gbis_gamma
BigReal alpha_cutoff
BigReal alpha_max
Bool LCPOOn
BigReal surface_tension
Bool drudeOn
Bool drudeHardWallOn
BigReal drudeTemp
BigReal drudeDamping
BigReal drudeBondLen
BigReal drudeBondConst
BigReal drudeNbtholeCut
Bool pairInteractionOn
int pairInteractionGroup1
int pairInteractionGroup2
Bool pairInteractionSelf
Bool cosAngles
Bool globalForcesOn
Bool tclForcesOn
Bool tclIsThreaded
Bool tclBCOn
char * tclBCScript
char tclBCArgs [128]
Bool freeEnergyOn
Bool miscForcesOn
Bool colvarsOn
Bool fixedAtomsOn
Bool fixedAtomsForces
Bool fixedAtomsForceOutput
Bool langevinOnAtStartup
Bool langevinOn
BigReal langevinTemp
BigReal langevinDamping
Bool langevinHydrogen
Bool langevin_useBAOAB
Bool loweAndersenOn
BigReal loweAndersenTemp
BigReal loweAndersenRate
BigReal loweAndersenCutoff
Bool globalOn
Bool dihedralOn
Bool COLDOn
BigReal COLDRate
BigReal COLDTemp
Bool tCoupleOn
BigReal tCoupleTemp
Bool stochRescaleOn
BigReal stochRescaleTemp
BigReal stochRescalePeriod
int stochRescaleFreq
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
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 1041 of file SimParameters.h.

01041 : mgridforcelist(), parseopts(0) {};

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

Definition at line 1042 of file SimParameters.h.

References initialize_config_data().

01042                                                  : mgridforcelist(), parseopts(0) {
01043           initialize_config_data(c,cwd);
01044         };

SimParameters::~SimParameters (  )  [inline]

Definition at line 1045 of file SimParameters.h.

01045 {};


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 7243 of file SimParameters.C.

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

07243                                                          {
07244   // Convenience function for staggered lambda scaling
07245   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
07246 }

BigReal SimParameters::getCurrentLambda ( const int  step  ) 

Definition at line 7190 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().

07190                                                       {
07191   /*Get lambda at the current step. 
07192 
07193    If alchLambdaFreq = 0, return alchLambda. For positive values of 
07194    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
07195    alchLambda2:
07196 
07197    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
07198 
07199    n - the current time step
07200    n0 - step at which switching begins (default = 0)
07201    N - total steps in the simulation
07202    dn - alchLambdaFreq (increment frequency, in steps)
07203    l/l2 - alchLambda/alchLambda2
07204  
07205    Note that each step _begins_ by incrementing alchLambda and then integrates
07206    in time. This means that the first and last switch steps may not behave as
07207    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
07208    no step occurs because alchLambda2 has already been reached.
07209   */
07210   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
07211     if ( step == N ) {
07212       return alchLambda2;
07213     }
07214     else {
07215       const int timeOrigin = firstTimestep + alchEquilSteps;
07216       const BigReal alchLambdaDelta = getLambdaDelta();
07217       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
07218       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
07219     }
07220   }
07221   else {
07222     return alchLambda;
07223   }
07224 }

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

Definition at line 7232 of file SimParameters.C.

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

07232                                                          {
07233   // Convenience function for staggered lambda scaling
07234   return (lambda <= alchElecLambdaStart ? 0.
07235           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
07236 }

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 7226 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, and firstTimestep.

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

07226                                           {
07227   // Increment by which Lambda changes.
07228   return ((alchLambda2 - alchLambda)*alchLambdaFreq
07229           / BigReal(N - firstTimestep - alchEquilSteps));
07230 }

BigReal SimParameters::getVdwLambda ( const BigReal  lambda  ) 

Definition at line 7238 of file SimParameters.C.

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

07238                                                         {
07239   // Convenience function for staggered lambda scaling
07240   return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
07241 }

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 1067 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

01067 { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (  )  [inline]

Definition at line 1068 of file SimParameters.h.

References proxyRecvSpanningTree.

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

01068 { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (  )  [inline]

Definition at line 1065 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

01065 { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (  )  [inline]

Definition at line 1066 of file SimParameters.h.

References proxySendSpanningTree.

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

01066 { 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 438 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

00438                                      {
00439     ComputeNonbondedUtil::select();
00440 }

void SimParameters::pme_select (  )  [static]

Definition at line 442 of file SimParameters.C.

References ComputePmeUtil::select().

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

00442                                {
00443   ComputePmeUtil::select();
00444 }

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

Definition at line 2360 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.

02360                                                                             {
02361 
02362      if ( ! latptr ) {
02363        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
02364      }
02365 
02366      ifstream xscFile(filename);
02367      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
02368 
02369      char labels[1024];
02370      do {
02371        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02372        xscFile.getline(labels,1023);
02373      } while ( strncmp(labels,"#$LABELS ",9) );
02374 
02375      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
02376      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
02377      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
02378      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
02379 
02380      int pos = 0;
02381      char *l_i = labels + 8;
02382      while ( *l_i ) {
02383        if ( *l_i == ' ' ) { ++l_i; continue; }
02384        char *l_i2;
02385        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
02386        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
02387          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
02388          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
02389          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
02390          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
02391          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
02392          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
02393          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
02394          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
02395          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
02396          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
02397          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
02398          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
02399          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
02400          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
02401          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
02402          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
02403          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
02404          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
02405        }
02406        ++pos;
02407        l_i = l_i2;
02408      }
02409      int numpos = pos;
02410 
02411      for ( pos = 0; pos < numpos; ++pos ) {
02412        double tmp;
02413        xscFile >> tmp;
02414        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02415        if ( pos == a_x ) cellBasisVector1.x = tmp;
02416        if ( pos == a_y ) cellBasisVector1.y = tmp;
02417        if ( pos == a_z ) cellBasisVector1.z = tmp;
02418        if ( pos == b_x ) cellBasisVector2.x = tmp;
02419        if ( pos == b_y ) cellBasisVector2.y = tmp;
02420        if ( pos == b_z ) cellBasisVector2.z = tmp;
02421        if ( pos == c_x ) cellBasisVector3.x = tmp;
02422        if ( pos == c_y ) cellBasisVector3.y = tmp;
02423        if ( pos == c_z ) cellBasisVector3.z = tmp;
02424        if ( pos == o_x ) cellOrigin.x = tmp;
02425        if ( pos == o_y ) cellOrigin.y = tmp;
02426        if ( pos == o_z ) cellOrigin.z = tmp;
02427        if ( pos == s_u ) strainRate2.x = tmp;
02428        if ( pos == s_v ) strainRate2.y = tmp;
02429        if ( pos == s_w ) strainRate2.z = tmp;
02430        if ( pos == s_x ) strainRate.x = tmp;
02431        if ( pos == s_y ) strainRate.y = tmp;
02432        if ( pos == s_z ) strainRate.z = tmp;
02433      }
02434 
02435    if ( latptr ) {
02436      Lattice test;
02437      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02438     
02439      if ( test.a_p() && ! lattice.a_p() ) {
02440        NAMD_die("cellBasisVector1 added during atom reinitialization");
02441      }
02442      if ( lattice.a_p() && ! test.a_p() ) {
02443        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
02444      }
02445      if ( test.b_p() && ! lattice.b_p() ) {
02446        NAMD_die("cellBasisVector2 added during atom reinitialization");
02447      }
02448      if ( lattice.b_p() && ! test.b_p() ) {
02449        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
02450      }
02451      if ( test.c_p() && ! lattice.c_p() ) {
02452        NAMD_die("cellBasisVector3 added during atom reinitialization");
02453      }
02454      if ( lattice.c_p() && ! test.c_p() ) {
02455        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
02456      }
02457 
02458      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02459    }
02460 
02461 }

void SimParameters::receive_SimParameters ( MIStream msg  ) 

Definition at line 7093 of file SimParameters.C.

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

07095 {
07096   msg->get(sizeof(SimParameters),(char*)this);
07097   if ( FFTWWisdomString ) {
07098     int fftwlen;
07099     msg->get(fftwlen);
07100     FFTWWisdomString = new char[fftwlen];
07101     msg->get(fftwlen,FFTWWisdomString);
07102 #ifdef NAMD_FFTW
07103 #ifdef NAMD_FFTW_3
07104     fftwf_import_wisdom_from_string(FFTWWisdomString);
07105 #else
07106     fftw_import_wisdom_from_string(FFTWWisdomString);
07107 #endif
07108 #endif
07109   }
07110   if ( tclBCScript ) {
07111     int tcllen;
07112     msg->get(tcllen);
07113     tclBCScript = new char[tcllen];
07114     msg->get(tcllen,tclBCScript);
07115   }
07116 
07117 #ifdef MEM_OPT_VERSION
07118   int filelen;
07119   msg->get(filelen);
07120   binAtomFile = new char[filelen];
07121   msg->get(filelen, binAtomFile);
07122   
07123   msg->get(filelen);
07124   binCoorFile = new char[filelen];
07125   msg->get(filelen, binCoorFile);
07126 
07127   if(binVelFile) {    
07128     msg->get(filelen);
07129     binVelFile = new char[filelen];
07130     msg->get(filelen, binVelFile);
07131   }
07132 
07133   if(binRefFile) {    
07134     msg->get(filelen);
07135     binRefFile = new char[filelen];
07136     msg->get(filelen, binRefFile);
07137   }
07138 #endif
07139 
07140 
07141   // The simParameters bit copy above put illegal values in the list pointers
07142   // So this resets everything so that unpacking will work.
07143   mgridforcelist.clear();
07144   mgridforcelist.unpack_data(msg);
07145   
07146   delete msg;
07147 }

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, alchDispLambda, alchElecLambda, alchEquilSteps, alchFepElecOn, alchFepOn, alchFepOnAtStartup, alchFepWCADispOn, alchFepWCArcut1, alchFepWCArcut2, alchFepWCArcut3, alchFepWCARepuOn, alchLambda, alchLambda2, alchLambdaFreq, alchLambdaIDWS, alchOn, alchOnAtStartup, alchRepLambda, alchThermIntOn, alchThermIntOnAtStartup, atobool(), berendsenPressureCompressibility, berendsenPressureOn, berendsenPressureRelaxationTime, berendsenPressureTarget, close_dcdfile(), close_veldcdfile(), commOnly, consForceScaling, constraintScaling, dcdFilename, dcdFrequency, drudeBondConst, drudeBondLen, drudeHardWallOn, eField, eFieldFreq, eFieldPhase, firstTimestep, fixCellDims, fixCellDimX, fixCellDimY, fixCellDimZ, fixedAtomsForces, fixedAtomsOn, 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,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00300     alchRepLambda = atof(value);
00301     alchFepWCARepuOn = true;
00302     alchFepWCADispOn = false;
00303     alchFepElecOn    = false;
00304     ComputeNonbondedUtil::select();
00305     return;
00306   }
00307 
00308   if ( ! strncasecmp(param,"alchDispLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00309     alchDispLambda = atof(value);
00310     alchFepWCARepuOn = false;
00311     alchFepWCADispOn = true;
00312     alchFepElecOn    = false;
00313     ComputeNonbondedUtil::select();
00314     return;
00315   }
00316 
00317   if ( ! strncasecmp(param,"alchElecLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00318     alchElecLambda = atof(value);
00319     alchFepWCARepuOn = false;
00320     alchFepWCADispOn = false;
00321     alchFepElecOn    = true;
00322     ComputeNonbondedUtil::select();
00323     return;
00324   }
00325 
00326 
00327   if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) {
00328     alchFepWCArcut1 = atof(value);
00329     ComputeNonbondedUtil::select();
00330     return;
00331   }
00332 
00333   if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) {
00334     alchFepWCArcut2 = atof(value);
00335     ComputeNonbondedUtil::select();
00336     return;
00337   }
00338 
00339   if ( ! strncasecmp(param,"alchFepWCArcut3",MAX_SCRIPT_PARAM_SIZE) ) {
00340     alchFepWCArcut3 = atof(value);
00341     ComputeNonbondedUtil::select();
00342     return;
00343   }
00344 
00345   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00346     alchLambda = atof(value);
00347     if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
00348       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00349     }
00350     ComputeNonbondedUtil::select();
00351     return;
00352   }
00353 
00354   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00355     alchLambda2 = atof(value);
00356     if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
00357       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00358     }
00359     ComputeNonbondedUtil::select();
00360     return;
00361   }
00362 
00363   if ( ! strncasecmp(param,"alchLambdaIDWS",MAX_SCRIPT_PARAM_SIZE) ) {
00364     alchLambdaIDWS = atof(value);
00365     setupIDWS();
00366     ComputeNonbondedUtil::select();
00367     return;
00368   }
00369 
00370   if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
00371     alchLambdaFreq = atoi(value);
00372     if ( alchLambdaIDWS >= 0 ) {
00373       NAMD_die("alchLambdaIDWS and alchLambdaFreq are not compatible.\n");
00374     }
00375     ComputeNonbondedUtil::select();
00376     return;
00377   }
00378 //fepe
00379 
00380   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00381     nonbondedScaling = atof(value);
00382     ComputeNonbondedUtil::select();
00383     return;
00384   }
00385 
00386   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00387     commOnly = atobool(value);
00388     ComputeNonbondedUtil::select();
00389     return;
00390   }
00391 
00392   // REST2 - We don't have to make any changes to ComputeNonbondedUtil
00393   // other than recalculating the LJTable.  Skip doing the other stuff.
00394   if ( ! strncasecmp(param,"soluteScalingFactor",MAX_SCRIPT_PARAM_SIZE)) {
00395     soluteScalingFactor = atof(value);
00396     if (soluteScalingFactor < 0.0) {
00397       NAMD_die("Solute scaling factor should be non-negative\n");
00398     }
00399     soluteScalingFactorCharge = soluteScalingFactor;
00400     soluteScalingFactorVdw = soluteScalingFactor;
00401     // update LJTable for CPU
00402     ComputeNonbondedUtil::select();
00403 #ifdef NAMD_CUDA
00404     // update LJTable for GPU, needs CPU update first
00405     ComputeCUDAMgr::getComputeCUDAMgr()->update();
00406 #endif
00407     return;
00408   }
00409   if ( ! strncasecmp(param,"soluteScalingFactorVdw",MAX_SCRIPT_PARAM_SIZE)) {
00410     soluteScalingFactorVdw = atof(value);
00411     if (soluteScalingFactorVdw < 0.0) {
00412       NAMD_die("Solute scaling factor for van der Waals "
00413           "should be non-negative\n");
00414     }
00415     // update LJTable for CPU
00416     ComputeNonbondedUtil::select();
00417 #ifdef NAMD_CUDA
00418     // update LJTable for GPU, needs CPU update first
00419     ComputeCUDAMgr::getComputeCUDAMgr()->update();
00420 #endif
00421     return;
00422   }
00423   if ( ! strncasecmp(param,"soluteScalingFactorCharge",MAX_SCRIPT_PARAM_SIZE)) {
00424     soluteScalingFactorCharge = atof(value);
00425     if (soluteScalingFactorCharge < 0.0) {
00426       NAMD_die("Solute scaling factor for electrostatics "
00427           "should be non-negative\n");
00428     }
00429     return;
00430   }
00431 
00432   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00433   sprintf(error,"Setting parameter %s from script failed!\n",param);
00434   NAMD_die(error);
00435 
00436 }

void SimParameters::send_SimParameters ( MOStream msg  ) 

Definition at line 7035 of file SimParameters.C.

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

07037 {
07038   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
07039   if ( msg == NULL )
07040   {
07041     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
07042   }*/
07043 
07044   msg->put(sizeof(SimParameters),(char*)this);
07045   if ( FFTWWisdomString ) {
07046     int fftwlen = strlen(FFTWWisdomString) + 1;
07047     msg->put(fftwlen);
07048     msg->put(fftwlen,FFTWWisdomString);
07049   }
07050   if ( tclBCScript ) {
07051     int tcllen = strlen(tclBCScript) + 1;
07052     msg->put(tcllen);
07053     msg->put(tcllen,tclBCScript);
07054   }
07055 
07056 #ifdef MEM_OPT_VERSION
07057   int filelen = strlen(binAtomFile)+1;
07058   msg->put(filelen);
07059   msg->put(filelen, binAtomFile);
07060 
07061   filelen = strlen(binCoorFile)+1;
07062   msg->put(filelen);
07063   msg->put(filelen, binCoorFile);
07064 
07065   if(binVelFile) {
07066     filelen = strlen(binVelFile)+1;
07067     msg->put(filelen);
07068     msg->put(filelen, binVelFile);
07069   }
07070 
07071   if(binRefFile) {
07072     filelen = strlen(binRefFile)+1;
07073     msg->put(filelen);
07074     msg->put(filelen, binRefFile);
07075   }
07076 #endif
07077 
07078   mgridforcelist.pack_data(msg);
07079   
07080   msg->end();
07081 }

int SimParameters::setupIDWS (  ) 

Definition at line 7162 of file SimParameters.C.

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

Referenced by scriptSet().

07162                              {
07163   if (alchLambdaIDWS < 0.) return 0;
07164   if (alchLambdaIDWS > 1.) {
07165     NAMD_die("alchLambdaIDWS should be either in the range [0.0, 1.0], or negative (disabled).\n");
07166   }
07167  /* 
07168   * The internal parameter alchIDWSFreq determines the number of steps of MD
07169   * before each switch of the value of alchLambda2. At most this occurs every
07170   * time the energy is evaluated and thus the default is the greater of
07171   * fullElectFrequency and nonbondedFrequency. However, this choice fails to
07172   * report alternating values if output is printed less often than every step
07173   * (which is almost certainly true). Thus the frequency is reset to match
07174   * alchOutFreq or, if that is zero, outputEnergies. Note that, if 
07175   * alchOutFreq > 0 but != outputEnergies, then the data going to stdout
07176   * are likely not useful since the comparison value is difficult to infer.
07177   */
07178   alchIDWSFreq = fullElectFrequency > 0 ? fullElectFrequency : nonbondedFrequency;
07179   if ( !alchOutFreq && outputEnergies > alchIDWSFreq ) alchIDWSFreq = outputEnergies;
07180   if ( alchOutFreq > alchIDWSFreq ) alchIDWSFreq = alchOutFreq;
07181   if ( alchOutFreq && alchOutFreq != outputEnergies) {
07182     iout << iWARN << "alchOutFreq and outputEnergies do not match. IDWS ouput"
07183          << " to stdout may not be useful!\n" << endi;
07184   }
07185   return 1;
07186 }


Member Data Documentation

Definition at line 958 of file SimParameters.h.

Definition at line 615 of file SimParameters.h.

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

Definition at line 614 of file SimParameters.h.

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

Definition at line 611 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 619 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 623 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 621 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 624 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 622 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 620 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 629 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 627 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Definition at line 628 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 625 of file SimParameters.h.

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

Definition at line 612 of file SimParameters.h.

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

Definition at line 613 of file SimParameters.h.

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

Definition at line 617 of file SimParameters.h.

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

Definition at line 616 of file SimParameters.h.

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

Definition at line 640 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 641 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 643 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 633 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 642 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 634 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

Definition at line 637 of file SimParameters.h.

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

Definition at line 646 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 636 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 649 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Definition at line 645 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

Definition at line 647 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 639 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 638 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Definition at line 426 of file SimParameters.h.

Referenced by CrosstermElem::computeForce().

Definition at line 420 of file SimParameters.h.

Definition at line 409 of file SimParameters.h.

Referenced by ComputePmeUtil::select().

Definition at line 404 of file SimParameters.h.

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

Definition at line 376 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 385 of file SimParameters.h.

Definition at line 375 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 405 of file SimParameters.h.

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

Definition at line 377 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 415 of file SimParameters.h.

Definition at line 407 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 979 of file SimParameters.h.

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

Definition at line 200 of file SimParameters.h.

Definition at line 673 of file SimParameters.h.

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

Definition at line 675 of file SimParameters.h.

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

Definition at line 674 of file SimParameters.h.

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

Definition at line 672 of file SimParameters.h.

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

Definition at line 217 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Definition at line 215 of file SimParameters.h.

Definition at line 1017 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1018 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1020 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 1019 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 793 of file SimParameters.h.

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

Definition at line 116 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 117 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 118 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 119 of file SimParameters.h.

Referenced by readExtendedSystem().

Definition at line 574 of file SimParameters.h.

Definition at line 576 of file SimParameters.h.

Definition at line 577 of file SimParameters.h.

Definition at line 1026 of file SimParameters.h.

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

Definition at line 870 of file SimParameters.h.

Definition at line 871 of file SimParameters.h.

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

Definition at line 331 of file SimParameters.h.

Definition at line 329 of file SimParameters.h.

Definition at line 333 of file SimParameters.h.

Referenced by ComputeConsTorque::doForce().

Definition at line 332 of file SimParameters.h.

Definition at line 334 of file SimParameters.h.

Definition at line 252 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 280 of file SimParameters.h.

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

Definition at line 271 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 271 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 271 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 540 of file SimParameters.h.

Referenced by Parameters::Parameters().

Definition at line 840 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 845 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 846 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 847 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 848 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 843 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 844 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 837 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 841 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 842 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 839 of file SimParameters.h.

Referenced by ComputeCylindricalBC::ComputeCylindricalBC().

Definition at line 965 of file SimParameters.h.

Definition at line 965 of file SimParameters.h.

Definition at line 965 of file SimParameters.h.

Definition at line 201 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 191 of file SimParameters.h.

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

Definition at line 193 of file SimParameters.h.

Referenced by Output::coordinate().

Definition at line 961 of file SimParameters.h.

Definition at line 961 of file SimParameters.h.

Definition at line 961 of file SimParameters.h.

Definition at line 573 of file SimParameters.h.

Definition at line 153 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

Definition at line 958 of file SimParameters.h.

Definition at line 958 of file SimParameters.h.

Definition at line 532 of file SimParameters.h.

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

Definition at line 528 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 533 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 527 of file SimParameters.h.

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

Definition at line 852 of file SimParameters.h.

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

Definition at line 853 of file SimParameters.h.

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

Definition at line 851 of file SimParameters.h.

Referenced by ComputeEField::doForce().

Definition at line 850 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 854 of file SimParameters.h.

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

Definition at line 186 of file SimParameters.h.

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

Definition at line 451 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 452 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 450 of file SimParameters.h.

Referenced by ComputeExtMgr::recvCoord().

Definition at line 449 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 866 of file SimParameters.h.

Definition at line 867 of file SimParameters.h.

Definition at line 808 of file SimParameters.h.

Definition at line 809 of file SimParameters.h.

Definition at line 810 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Definition at line 130 of file SimParameters.h.

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

Definition at line 555 of file SimParameters.h.

Referenced by CollectionMgr::submitForces().

Definition at line 713 of file SimParameters.h.

Definition at line 712 of file SimParameters.h.

Definition at line 710 of file SimParameters.h.

Definition at line 711 of file SimParameters.h.

Definition at line 126 of file SimParameters.h.

Definition at line 757 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Definition at line 758 of file SimParameters.h.

Referenced by ComputeFmmSerialMgr::recvCoord().

Definition at line 203 of file SimParameters.h.

Definition at line 196 of file SimParameters.h.

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

Definition at line 549 of file SimParameters.h.

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

Definition at line 512 of file SimParameters.h.

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

Definition at line 1001 of file SimParameters.h.

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

Definition at line 541 of file SimParameters.h.

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

Definition at line 572 of file SimParameters.h.

Definition at line 291 of file SimParameters.h.

Definition at line 290 of file SimParameters.h.

Definition at line 263 of file SimParameters.h.

Definition at line 258 of file SimParameters.h.

Definition at line 259 of file SimParameters.h.

Definition at line 260 of file SimParameters.h.

Definition at line 262 of file SimParameters.h.

Definition at line 255 of file SimParameters.h.

Definition at line 257 of file SimParameters.h.

Definition at line 261 of file SimParameters.h.

Definition at line 256 of file SimParameters.h.

Definition at line 984 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 958 of file SimParameters.h.

Definition at line 902 of file SimParameters.h.

Referenced by HomePatch::doGroupSizeCheck().

Definition at line 134 of file SimParameters.h.

Referenced by NamdHybridLB::NamdHybridLB().

Definition at line 948 of file SimParameters.h.

Definition at line 899 of file SimParameters.h.

Definition at line 969 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

Definition at line 516 of file SimParameters.h.

Definition at line 560 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 561 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 557 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 678 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

Definition at line 132 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

Definition at line 127 of file SimParameters.h.

Referenced by LdbCoordinator::createLoadBalancer().

Definition at line 135 of file SimParameters.h.

Definition at line 137 of file SimParameters.h.

Definition at line 129 of file SimParameters.h.

Referenced by LdbCoordinator::initialize().

Definition at line 136 of file SimParameters.h.

Definition at line 138 of file SimParameters.h.

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

Definition at line 128 of file SimParameters.h.

Referenced by LdbCoordinator::initialize(), and NamdCentLB::Strategy().

Definition at line 170 of file SimParameters.h.

Definition at line 171 of file SimParameters.h.

Definition at line 168 of file SimParameters.h.

Definition at line 169 of file SimParameters.h.

Definition at line 433 of file SimParameters.h.

Definition at line 226 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 1028 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 108 of file SimParameters.h.

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

Definition at line 896 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 569 of file SimParameters.h.

Definition at line 566 of file SimParameters.h.

Referenced by Sequencer::integrate().

Definition at line 568 of file SimParameters.h.

Definition at line 567 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 1005 of file SimParameters.h.

Referenced by Node::startup().

Definition at line 220 of file SimParameters.h.

Referenced by HomePatch::doMarginCheck().

Definition at line 236 of file SimParameters.h.

Definition at line 234 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 936 of file SimParameters.h.

Definition at line 822 of file SimParameters.h.

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

Definition at line 924 of file SimParameters.h.

Definition at line 167 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 922 of file SimParameters.h.

Definition at line 888 of file SimParameters.h.

Referenced by Controller::printEnergies().

Definition at line 1036 of file SimParameters.h.

Definition at line 1031 of file SimParameters.h.

Definition at line 1033 of file SimParameters.h.

Definition at line 1034 of file SimParameters.h.

Definition at line 1032 of file SimParameters.h.

Definition at line 1037 of file SimParameters.h.

Definition at line 1035 of file SimParameters.h.

Definition at line 934 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 819 of file SimParameters.h.

Definition at line 816 of file SimParameters.h.

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

Definition at line 821 of file SimParameters.h.

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

Definition at line 820 of file SimParameters.h.

Referenced by Controller::minimize().

Definition at line 818 of file SimParameters.h.

Definition at line 817 of file SimParameters.h.

Referenced by Controller::minimize().

Definition at line 550 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 906 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

Definition at line 905 of file SimParameters.h.

Referenced by HomePatch::mollyAverage().

Definition at line 311 of file SimParameters.h.

Definition at line 313 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

Definition at line 314 of file SimParameters.h.

Definition at line 297 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 299 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 725 of file SimParameters.h.

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

Definition at line 735 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 736 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 737 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 739 of file SimParameters.h.

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

Definition at line 731 of file SimParameters.h.

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

Definition at line 741 of file SimParameters.h.

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

Definition at line 721 of file SimParameters.h.

Definition at line 754 of file SimParameters.h.

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

Definition at line 748 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 747 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 750 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 749 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 752 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 751 of file SimParameters.h.

Referenced by ComputeMsmMgr::initialize().

Definition at line 893 of file SimParameters.h.

Referenced by Sequencer::integrate().

Definition at line 689 of file SimParameters.h.

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

Definition at line 122 of file SimParameters.h.

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

Definition at line 174 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 173 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 172 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 930 of file SimParameters.h.

Definition at line 932 of file SimParameters.h.

Definition at line 926 of file SimParameters.h.

Definition at line 928 of file SimParameters.h.

Definition at line 1016 of file SimParameters.h.

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

Definition at line 1024 of file SimParameters.h.

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

Definition at line 141 of file SimParameters.h.

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

Definition at line 882 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::finishReductions().

Definition at line 149 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

Definition at line 876 of file SimParameters.h.

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

Definition at line 248 of file SimParameters.h.

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

Definition at line 938 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Definition at line 885 of file SimParameters.h.

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

Definition at line 879 of file SimParameters.h.

Referenced by Controller::printTiming().

Definition at line 536 of file SimParameters.h.

Definition at line 537 of file SimParameters.h.

Definition at line 238 of file SimParameters.h.

Definition at line 246 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Definition at line 240 of file SimParameters.h.

Definition at line 245 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Definition at line 244 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects().

Definition at line 247 of file SimParameters.h.

Referenced by HomePatch::doPairlistCheck().

Definition at line 771 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 762 of file SimParameters.h.

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

Definition at line 767 of file SimParameters.h.

Definition at line 770 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 769 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 772 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 773 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 774 of file SimParameters.h.

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

Definition at line 776 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 775 of file SimParameters.h.

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

Definition at line 768 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize().

Definition at line 778 of file SimParameters.h.

Referenced by ComputePmeMgr::initialize_pencils().

Definition at line 761 of file SimParameters.h.

Definition at line 699 of file SimParameters.h.

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

Definition at line 700 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 701 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 702 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

Definition at line 697 of file SimParameters.h.

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

Definition at line 507 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Definition at line 1006 of file SimParameters.h.

Definition at line 1010 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

Definition at line 1009 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

Definition at line 1012 of file SimParameters.h.

Referenced by Node::startup().

Definition at line 465 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 475 of file SimParameters.h.

Definition at line 476 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 474 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 480 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 479 of file SimParameters.h.

Definition at line 477 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

Definition at line 478 of file SimParameters.h.

Definition at line 459 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 463 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 462 of file SimParameters.h.

Definition at line 464 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 500 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 501 of file SimParameters.h.

Definition at line 490 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 503 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

Definition at line 460 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 470 of file SimParameters.h.

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

Definition at line 495 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 498 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 497 of file SimParameters.h.

Definition at line 496 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 472 of file SimParameters.h.

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

Definition at line 489 of file SimParameters.h.

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

Definition at line 504 of file SimParameters.h.

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

Definition at line 457 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 458 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 485 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 484 of file SimParameters.h.

Definition at line 491 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 481 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 483 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 482 of file SimParameters.h.

Definition at line 505 of file SimParameters.h.

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

Definition at line 468 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 469 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 471 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 466 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 467 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Definition at line 486 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

Definition at line 461 of file SimParameters.h.

Definition at line 488 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Definition at line 980 of file SimParameters.h.

Referenced by buildExclusions().

Definition at line 940 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 213 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Definition at line 214 of file SimParameters.h.

Definition at line 304 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 305 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 302 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 306 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 321 of file SimParameters.h.

Definition at line 319 of file SimParameters.h.

Definition at line 323 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

Definition at line 322 of file SimParameters.h.

Definition at line 324 of file SimParameters.h.

Definition at line 188 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 991 of file SimParameters.h.

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

Definition at line 992 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 993 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 994 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 996 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 998 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 269 of file SimParameters.h.

Referenced by ComputeRestraints::ComputeRestraints().

Definition at line 152 of file SimParameters.h.

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

Definition at line 341 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 344 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 342 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 343 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 339 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 345 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 340 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

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

Definition at line 447 of file SimParameters.h.

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

scaling factor for solute interactions

Definition at line 439 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 441 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 444 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 834 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 835 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 828 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 830 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 825 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 832 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 833 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 827 of file SimParameters.h.

Referenced by ComputeSphericalBC::ComputeSphericalBC().

Definition at line 277 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

Definition at line 278 of file SimParameters.h.

Referenced by ComputeRestraints::doForce().

Definition at line 901 of file SimParameters.h.

Definition at line 919 of file SimParameters.h.

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

Definition at line 862 of file SimParameters.h.

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

Definition at line 857 of file SimParameters.h.

Definition at line 861 of file SimParameters.h.

Referenced by ComputeStir::doForce().

Definition at line 863 of file SimParameters.h.

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

Definition at line 859 of file SimParameters.h.

Definition at line 860 of file SimParameters.h.

How frequently (time steps) stochastic velocity rescaling occurs.

Definition at line 597 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 600 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 584 of file SimParameters.h.

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

Timescale (ps) for stochastic velocity rescaling.

Definition at line 594 of file SimParameters.h.

Referenced by Controller::Controller().

Temperature for stochastic velocity rescaling.

Definition at line 591 of file SimParameters.h.

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

Definition at line 1027 of file SimParameters.h.

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

Definition at line 704 of file SimParameters.h.

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

Definition at line 705 of file SimParameters.h.

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

Definition at line 523 of file SimParameters.h.

Referenced by ComputeLCPO::ComputeLCPO().

Definition at line 369 of file SimParameters.h.

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 367 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 368 of file SimParameters.h.

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 370 of file SimParameters.h.

Definition at line 366 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 366 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

Definition at line 352 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 354 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 350 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 353 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 349 of file SimParameters.h.

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

Definition at line 351 of file SimParameters.h.

Referenced by Parameters::read_ener_table().

Definition at line 548 of file SimParameters.h.

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

Definition at line 546 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 544 of file SimParameters.h.

Referenced by ComputeTclBC::ComputeTclBC().

Definition at line 917 of file SimParameters.h.

Definition at line 358 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 360 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 360 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 363 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 362 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 363 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 359 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 362 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 358 of file SimParameters.h.

Referenced by ComputeMgr::createComputes().

Definition at line 361 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Definition at line 921 of file SimParameters.h.

Definition at line 140 of file SimParameters.h.

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

Definition at line 164 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 165 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 166 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Definition at line 951 of file SimParameters.h.

Definition at line 1000 of file SimParameters.h.

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

Definition at line 663 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 788 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 799 of file SimParameters.h.

Definition at line 781 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Definition at line 242 of file SimParameters.h.

Definition at line 1003 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 784 of file SimParameters.h.

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

Definition at line 230 of file SimParameters.h.

Referenced by ComputeNonbondedUtil::select().

Definition at line 987 of file SimParameters.h.

Definition at line 981 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Definition at line 202 of file SimParameters.h.

Referenced by scriptSet().

Definition at line 194 of file SimParameters.h.

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

Definition at line 154 of file SimParameters.h.

Referenced by recursive_bisect_with_curve().

Definition at line 184 of file SimParameters.h.

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

Definition at line 204 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Definition at line 198 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Definition at line 180 of file SimParameters.h.

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

Definition at line 181 of file SimParameters.h.

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


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

Generated on 16 Jan 2019 for NAMD by  doxygen 1.6.1