SimParameters Class Reference

#include <SimParameters.h>

List of all members.

Public Member Functions

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

Static Public Member Functions

static void nonbonded_select ()

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 alchOn
Bool alchFepOn
Bool alchThermIntOn
Bool alchFepWCARepuOn
Bool alchFepWCADispOn
Bool alchFepElecOn
Bool alchFepWhamOn
int alchMethod
BigReal alchLambda
BigReal alchLambda2
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 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
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 useOptPME
Bool useManyToMany
Bool FFTWEstimate
Bool FFTWPatient
Bool FFTWUseWisdom
char FFTWWisdomFile [128]
char * FFTWWisdomString
Bool minimizeCGOn
Bool minVerbose
BigReal minTinyStep
BigReal minBabyStep
BigReal minLineGoal
Bool minimizeOn
BigReal maximumMove
Bool sphericalBCOn
zVector sphericalCenter
BigReal sphericalBCk1
BigReal sphericalBCk2
BigReal sphericalBCr1
BigReal sphericalBCr2
int sphericalBCexp1
int sphericalBCexp2
Bool cylindricalBCOn
zVector cylindricalCenter
char cylindricalBCAxis
BigReal cylindricalBCr1
BigReal cylindricalBCr2
BigReal cylindricalBCl1
BigReal cylindricalBCl2
int cylindricalBCexp1
int cylindricalBCexp2
BigReal cylindricalBCk1
BigReal cylindricalBCk2
Bool eFieldOn
Bool eFieldNormalized
zVector eField
BigReal eFieldFreq
BigReal eFieldPhase
Bool stirOn
char stirFilename [128]
BigReal stirStartingTheta
BigReal stirVel
BigReal stirK
zVector stirAxis
zVector stirPivot
Bool extraBondsOn
Bool consForceOn
char consForceFile [128]
BigReal consForceScaling
int outputEnergies
int outputMomenta
int outputTiming
int outputCudaTiming
int outputPressure
Bool mergeCrossterms
int firstTimestep
MTSChoices MTSAlgorithm
int longSplitting
Bool ignoreMass
int splitPatch
BigReal hgroupCutoff
int mollyOn
BigReal mollyTol
int mollyIter
int rigidBonds
BigReal rigidTol
int rigidIter
int rigidDie
Bool useSettle
Bool testOn
Bool commOnly
Bool statsOn
int totalAtoms
int maxSelfPart
int maxPairPart
int numAtomsSelf
int numAtomsSelf2
int numAtomsPair
int numAtomsPair2
int minAtomsPerPatch
int maxExclusionFlags
Bool outputPatchDetails
Bool staticAtomAssignment
Bool replicaUniformPatchGrids
Bool HydrogenBonds
Bool useAntecedent
int aaAngleExp
int haAngleExp
int distAttExp
int distRepExp
BigReal dhaCutoffAngle
BigReal dhaOnAngle
BigReal dhaOffAngle
BigReal daCutoffDist
BigReal daOnDist
BigReal daOffDist
int IMDon
int IMDport
int IMDfreq
int IMDwait
int IMDignore
int IMDignoreForces
Bool amberOn
Bool readExclusions
BigReal vdwscale14
Bool gromacsOn
Bool vdwGeometricSigma
BigReal scriptArg1
BigReal scriptArg2
BigReal scriptArg3
BigReal scriptArg4
BigReal scriptArg5
int scriptIntArg1
int scriptIntArg2
char scriptStringArg1 [128]
char scriptStringArg2 [128]
Bool useCompressedPsf
Bool genCompressedPsf
Bool usePluginIO
Bool mallocTest
Bool printExclusions
int proxySendSpanningTree
int proxyRecvSpanningTree
int proxyTreeBranchFactor
int numinputprocs
char * binAtomFile
char * binCoorFile
char * binVelFile
char * binRefFile
int numoutputprocs
int numoutputwrts
char computeMapFilename [128]
Bool storeComputeMap
Bool loadComputeMap
int mic_hostSplit
int mic_numParts_self_p1
int mic_numParts_pair_p1
int mic_numParts_pair_p2
int mic_unloadMICPEs
int mic_deviceThreshold
int mic_singleKernel


Detailed Description

Definition at line 100 of file SimParameters.h.


Constructor & Destructor Documentation

SimParameters::SimParameters (  )  [inline]

Definition at line 981 of file SimParameters.h.

00981 : mgridforcelist(), parseopts(0) {};

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

Definition at line 982 of file SimParameters.h.

References initialize_config_data().

00982                                                  : mgridforcelist(), parseopts(0) {
00983           initialize_config_data(c,cwd);
00984         };

SimParameters::~SimParameters (  )  [inline]

Definition at line 985 of file SimParameters.h.

00985 {};


Member Function Documentation

void SimParameters::close_dcdfile (  ) 

Definition at line 651 of file Output.C.

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

Referenced by scriptSet().

00651                                   {
00652 
00653   Output *output = Node::Object()->output;
00654   if ( ! output ) return;
00655 
00656   output->output_dcdfile(END_OF_RUN, 0, 0, 0);
00657 
00658 }

void SimParameters::close_veldcdfile (  ) 

Definition at line 660 of file Output.C.

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

Referenced by scriptSet().

00660                                      {
00661 
00662   Output *output = Node::Object()->output;
00663   if ( ! output ) return;
00664 
00665   output->output_veldcdfile(END_OF_RUN, 0, 0);
00666 
00667 }

BigReal SimParameters::getBondLambda ( const   BigReal  ) 

Definition at line 6981 of file SimParameters.C.

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

06981                                                          {
06982   // Convenience function for staggered lambda scaling
06983   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
06984 }

BigReal SimParameters::getCurrentLambda ( const   int  ) 

Definition at line 6928 of file SimParameters.C.

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

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

06928                                                       {
06929   /*Get lambda at the current step. 
06930 
06931    If alchLambdaFreq = 0, return alchLambda. For positive values of 
06932    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
06933    alchLambda2:
06934 
06935    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
06936 
06937    n - the current time step
06938    n0 - step at which switching begins (default = 0)
06939    N - total steps in the simulation
06940    dn - alchLambdaFreq (increment frequency, in steps)
06941    l/l2 - alchLambda/alchLambda2
06942  
06943    Note that each step _begins_ by incrementing alchLambda and then integrates
06944    in time. This means that the first and last switch steps may not behave as
06945    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
06946    no step occurs because alchLambda2 has already been reached.
06947   */
06948   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
06949     if ( step == N ) {
06950       return alchLambda2;
06951     }
06952     else {
06953       const int timeOrigin = firstTimestep + alchEquilSteps;
06954       const BigReal alchLambdaDelta = getLambdaDelta();
06955       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
06956       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
06957     }
06958   }
06959   else {
06960     return alchLambda;
06961   }
06962 }

BigReal SimParameters::getElecLambda ( const   BigReal  ) 

Definition at line 6970 of file SimParameters.C.

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

06970                                                          {
06971   // Convenience function for staggered lambda scaling
06972   return (lambda <= alchElecLambdaStart ? 0.
06973           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
06974 }

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

Definition at line 96 of file SimParameters.C.

References ParseOptions::getfromptr().

00096                                                                     {
00097   if ( parseopts ) return parseopts->getfromptr(name,outbuf);
00098   else return 0;
00099 }

BigReal SimParameters::getLambdaDelta ( void   ) 

Definition at line 6964 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, and firstTimestep.

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

06964                                           {
06965   // Increment by which Lambda changes.
06966   return ((alchLambda2 - alchLambda)*alchLambdaFreq
06967           / BigReal(N - firstTimestep - alchEquilSteps));
06968 }

BigReal SimParameters::getVdwLambda ( const   BigReal  ) 

Definition at line 6976 of file SimParameters.C.

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

06976                                                         {
06977   // Convenience function for staggered lambda scaling
06978   return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
06979 }

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

Definition at line 124 of file SimParameters.C.

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

Referenced by SimParameters().

00126 {
00127 
00128    parseopts = new ParseOptions;   //  Object to check consistency of config file
00129    ParseOptions &opts = *parseopts;
00130 
00131    config_parser(opts);
00132 
00134    if (!opts.check_consistency()) 
00135    {
00136       NAMD_die("Internal error in configuration file parser");
00137    }
00138 
00139    // Now, feed the object with the actual configuration options through the
00140    // ParseOptions file and make sure everything is OK
00141    if (!opts.set(*config)) 
00142    {
00143       NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00144    }
00145 
00147 
00148    check_config(opts,config,cwd);
00149 
00150    print_config(opts,config,cwd);
00151 
00152 }

int SimParameters::isRecvSpanningTreeOn (  )  [inline]

Definition at line 1006 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

01006 { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (  )  [inline]

Definition at line 1007 of file SimParameters.h.

References proxyRecvSpanningTree.

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

01007 { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (  )  [inline]

Definition at line 1004 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

01004 { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (  )  [inline]

Definition at line 1005 of file SimParameters.h.

References proxySendSpanningTree.

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

01005 { return proxySendSpanningTree == -1; }

int SimParameters::issetinparseopts ( const char *  name  ) 

Definition at line 106 of file SimParameters.C.

References ParseOptions::issetfromptr().

00106                                                     {
00107   if ( parseopts ) return parseopts->issetfromptr(name);
00108   else return -1;
00109 }

int SimParameters::istrueinparseopts ( const char *  name  ) 

Definition at line 101 of file SimParameters.C.

References ParseOptions::istruefromptr().

00101                                                      {
00102   if ( parseopts ) return parseopts->istruefromptr(name);
00103   else return -1;
00104 }

void SimParameters::nonbonded_select (  )  [static]

Definition at line 373 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

00373                                      {
00374     ComputeNonbondedUtil::select();
00375 }

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

Definition at line 2231 of file SimParameters.C.

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

02231                                                                             {
02232 
02233      if ( ! latptr ) {
02234        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
02235      }
02236 
02237      ifstream xscFile(filename);
02238      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
02239 
02240      char labels[1024];
02241      do {
02242        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02243        xscFile.getline(labels,1023);
02244      } while ( strncmp(labels,"#$LABELS ",9) );
02245 
02246      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
02247      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
02248      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
02249      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
02250 
02251      int pos = 0;
02252      char *l_i = labels + 8;
02253      while ( *l_i ) {
02254        if ( *l_i == ' ' ) { ++l_i; continue; }
02255        char *l_i2;
02256        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
02257        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
02258          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
02259          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
02260          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
02261          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
02262          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
02263          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
02264          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
02265          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
02266          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
02267          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
02268          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
02269          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
02270          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
02271          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
02272          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
02273          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
02274          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
02275          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
02276        }
02277        ++pos;
02278        l_i = l_i2;
02279      }
02280      int numpos = pos;
02281 
02282      for ( pos = 0; pos < numpos; ++pos ) {
02283        double tmp;
02284        xscFile >> tmp;
02285        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02286        if ( pos == a_x ) cellBasisVector1.x = tmp;
02287        if ( pos == a_y ) cellBasisVector1.y = tmp;
02288        if ( pos == a_z ) cellBasisVector1.z = tmp;
02289        if ( pos == b_x ) cellBasisVector2.x = tmp;
02290        if ( pos == b_y ) cellBasisVector2.y = tmp;
02291        if ( pos == b_z ) cellBasisVector2.z = tmp;
02292        if ( pos == c_x ) cellBasisVector3.x = tmp;
02293        if ( pos == c_y ) cellBasisVector3.y = tmp;
02294        if ( pos == c_z ) cellBasisVector3.z = tmp;
02295        if ( pos == o_x ) cellOrigin.x = tmp;
02296        if ( pos == o_y ) cellOrigin.y = tmp;
02297        if ( pos == o_z ) cellOrigin.z = tmp;
02298        if ( pos == s_u ) strainRate2.x = tmp;
02299        if ( pos == s_v ) strainRate2.y = tmp;
02300        if ( pos == s_w ) strainRate2.z = tmp;
02301        if ( pos == s_x ) strainRate.x = tmp;
02302        if ( pos == s_y ) strainRate.y = tmp;
02303        if ( pos == s_z ) strainRate.z = tmp;
02304      }
02305 
02306    if ( latptr ) {
02307      Lattice test;
02308      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02309     
02310      if ( test.a_p() && ! lattice.a_p() ) {
02311        NAMD_die("cellBasisVector1 added during atom reinitialization");
02312      }
02313      if ( lattice.a_p() && ! test.a_p() ) {
02314        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
02315      }
02316      if ( test.b_p() && ! lattice.b_p() ) {
02317        NAMD_die("cellBasisVector2 added during atom reinitialization");
02318      }
02319      if ( lattice.b_p() && ! test.b_p() ) {
02320        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
02321      }
02322      if ( test.c_p() && ! lattice.c_p() ) {
02323        NAMD_die("cellBasisVector3 added during atom reinitialization");
02324      }
02325      if ( lattice.c_p() && ! test.c_p() ) {
02326        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
02327      }
02328 
02329      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02330    }
02331 
02332 }

void SimParameters::receive_SimParameters ( MIStream  ) 

Definition at line 6870 of file SimParameters.C.

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

06872 {
06873   msg->get(sizeof(SimParameters),(char*)this);
06874   if ( FFTWWisdomString ) {
06875     int fftwlen;
06876     msg->get(fftwlen);
06877     FFTWWisdomString = new char[fftwlen];
06878     msg->get(fftwlen,FFTWWisdomString);
06879 #ifdef NAMD_FFTW
06880 #ifdef NAMD_FFTW_3
06881     fftwf_import_wisdom_from_string(FFTWWisdomString);
06882 #else
06883     fftw_import_wisdom_from_string(FFTWWisdomString);
06884 #endif
06885 #endif
06886   }
06887   if ( tclBCScript ) {
06888     int tcllen;
06889     msg->get(tcllen);
06890     tclBCScript = new char[tcllen];
06891     msg->get(tcllen,tclBCScript);
06892   }
06893 
06894 #ifdef MEM_OPT_VERSION
06895   int filelen;
06896   msg->get(filelen);
06897   binAtomFile = new char[filelen];
06898   msg->get(filelen, binAtomFile);
06899   
06900   msg->get(filelen);
06901   binCoorFile = new char[filelen];
06902   msg->get(filelen, binCoorFile);
06903 
06904   if(binVelFile) {    
06905     msg->get(filelen);
06906     binVelFile = new char[filelen];
06907     msg->get(filelen, binVelFile);
06908   }
06909 
06910   if(binRefFile) {    
06911     msg->get(filelen);
06912     binRefFile = new char[filelen];
06913     msg->get(filelen, binRefFile);
06914   }
06915 #endif
06916 
06917 
06918   // The simParameters bit copy above put illegal values in the list pointers
06919   // So this resets everything so that unpacking will work.
06920   mgridforcelist.clear();
06921   mgridforcelist.unpack_data(msg);
06922   
06923   delete msg;
06924 }

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

Definition at line 166 of file SimParameters.C.

References accelMDalpha, accelMDE, accelMDGRestartFile, accelMDGSigma0D, accelMDGSigma0P, accelMDTalpha, accelMDTE, alchDispLambda, alchElecLambda, alchEquilSteps, alchFepElecOn, alchFepWCADispOn, alchFepWCArcut1, alchFepWCArcut2, alchFepWCArcut3, alchFepWCARepuOn, alchLambda, alchLambda2, alchLambdaFreq, alchOn, alchOnAtStartup, alchRepLambda, 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, initialTemp, langevin_useBAOAB, langevinOn, langevinOnAtStartup, langevinPistonDecay, langevinPistonOn, langevinPistonPeriod, langevinPistonTarget, langevinPistonTemp, langevinTemp, loweAndersenTemp, MAX_SCRIPT_PARAM_SIZE, maximumMove, minimizeOn, N, NAMD_die(), nonbondedScaling, outputEnergies, outputFilename, 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, ComputeNonbondedUtil::select(), stirAxis, stirPivot, surfaceTensionTarget, tclBCArgs, useConstantArea, useConstantRatio, useFlexibleCell, useGroupPressure, and velDcdFilename.

Referenced by Node::scriptParam().

00166                                                                   {
00167 
00168   if ( CkMyRank() ) return;
00169 
00170 #define MAX_SCRIPT_PARAM_SIZE 128
00171 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00172 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00173 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00174 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
00175 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00176 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00177 
00178   SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00179   SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00180   SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00181   SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00182   SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00183   SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1)
00184   SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2)
00185   SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1)
00186   SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2)
00187   SCRIPT_PARSE_INT("numsteps",N)
00188   if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) {
00189     N = firstTimestep = atoi(value); return;
00190   }
00191   SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00192   SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00193   SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
00194   SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
00195   // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00196   if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) {
00197     langevinOn = atobool(value);
00198     if ( langevinOn && ! langevinOnAtStartup ) {
00199       NAMD_die("Langevin must be enabled at startup to disable and re-enable in script.");
00200     }
00201     return;
00202   }
00203   SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00204   SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
00205   SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
00206   SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00207   SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00208   SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00209   SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00210   SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
00211   SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
00212   SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
00213   SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
00214   SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00215   SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00216   SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
00217                         langevinPistonTarget,/PRESSUREFACTOR)
00218   SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00219   SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00220   SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00221   SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
00222                         surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
00223   SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00224   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
00225                         berendsenPressureTarget,/PRESSUREFACTOR)
00226   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
00227                         berendsenPressureCompressibility,*PRESSUREFACTOR)
00228   SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00229                                 berendsenPressureRelaxationTime)
00230   SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00231   SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00232   SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn)
00233   SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst)
00234   SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen)
00235   SCRIPT_PARSE_STRING("outputname",outputFilename)
00236   SCRIPT_PARSE_INT("outputEnergies",outputEnergies)
00237   SCRIPT_PARSE_STRING("restartname",restartFilename)
00238   SCRIPT_PARSE_INT("DCDfreq",dcdFrequency)
00239   if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
00240     close_dcdfile();  // *** implemented in Output.C ***
00241     strcpy(dcdFilename,value);
00242     return;
00243   }
00244   if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
00245     close_veldcdfile();  // *** implemented in Output.C ***
00246     strcpy(velDcdFilename,value);
00247     return;
00248   }
00249   SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00250   SCRIPT_PARSE_VECTOR("eField",eField)
00251   SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00252   SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
00253   SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 
00254   SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 
00255   SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 
00256   SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 
00257   SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 
00258   SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 
00259   SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile)
00260   SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00261   SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00262   if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
00263     NAMD_die("Can't yet modify mgridforcescale in a script");
00264     return;
00265   }
00266   if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
00267     NAMD_die("Can't yet modify mgridforcevoff in a script");
00268     return;
00269   }
00270    
00271   if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00272     if ( ! fixedAtomsOn )
00273       NAMD_die("FixedAtoms may not be enabled in a script.");
00274     if ( ! fixedAtomsForces )
00275       NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00276     fixedAtomsOn = atobool(value);
00277     return;
00278   }
00279 
00280 //fepb
00281   if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) {
00282     alchOn = atobool(value);
00283     if ( alchOn && ! alchOnAtStartup ) {
00284        NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script.");
00285     }
00286     ComputeNonbondedUtil::select();
00287     return;
00288   }
00289   SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
00290 
00291   if ( ! strncasecmp(param,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00292     alchRepLambda = atof(value);
00293     alchFepWCARepuOn = true;
00294     alchFepWCADispOn = false;
00295     alchFepElecOn    = false;
00296     ComputeNonbondedUtil::select();
00297     return;
00298   }
00299 
00300   if ( ! strncasecmp(param,"alchDispLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00301     alchDispLambda = atof(value);
00302     alchFepWCARepuOn = false;
00303     alchFepWCADispOn = true;
00304     alchFepElecOn    = false;
00305     ComputeNonbondedUtil::select();
00306     return;
00307   }
00308 
00309   if ( ! strncasecmp(param,"alchElecLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00310     alchElecLambda = atof(value);
00311     alchFepWCARepuOn = false;
00312     alchFepWCADispOn = false;
00313     alchFepElecOn    = true;
00314     ComputeNonbondedUtil::select();
00315     return;
00316   }
00317 
00318 
00319   if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) {
00320     alchFepWCArcut1 = atof(value);
00321     ComputeNonbondedUtil::select();
00322     return;
00323   }
00324 
00325   if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) {
00326     alchFepWCArcut2 = atof(value);
00327     ComputeNonbondedUtil::select();
00328     return;
00329   }
00330 
00331   if ( ! strncasecmp(param,"alchFepWCArcut3",MAX_SCRIPT_PARAM_SIZE) ) {
00332     alchFepWCArcut3 = atof(value);
00333     ComputeNonbondedUtil::select();
00334     return;
00335   }
00336 
00337   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00338     alchLambda = atof(value);
00339     ComputeNonbondedUtil::select();
00340     return;
00341   }
00342 
00343   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00344     alchLambda2 = atof(value);
00345     ComputeNonbondedUtil::select();
00346     return;
00347   }
00348 
00349   if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
00350     alchLambdaFreq = atoi(value);
00351     ComputeNonbondedUtil::select();
00352     return;
00353   }
00354 //fepe
00355 
00356   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00357     nonbondedScaling = atof(value);
00358     ComputeNonbondedUtil::select();
00359     return;
00360   }
00361   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00362     commOnly = atobool(value);
00363     ComputeNonbondedUtil::select();
00364     return;
00365   }
00366 
00367   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00368   sprintf(error,"Setting parameter %s from script failed!\n",param);
00369   NAMD_die(error);
00370 
00371 }

void SimParameters::send_SimParameters ( MOStream  ) 

Definition at line 6812 of file SimParameters.C.

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

06814 {
06815   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
06816   if ( msg == NULL )
06817   {
06818     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
06819   }*/
06820 
06821   msg->put(sizeof(SimParameters),(char*)this);
06822   if ( FFTWWisdomString ) {
06823     int fftwlen = strlen(FFTWWisdomString) + 1;
06824     msg->put(fftwlen);
06825     msg->put(fftwlen,FFTWWisdomString);
06826   }
06827   if ( tclBCScript ) {
06828     int tcllen = strlen(tclBCScript) + 1;
06829     msg->put(tcllen);
06830     msg->put(tcllen,tclBCScript);
06831   }
06832 
06833 #ifdef MEM_OPT_VERSION
06834   int filelen = strlen(binAtomFile)+1;
06835   msg->put(filelen);
06836   msg->put(filelen, binAtomFile);
06837 
06838   filelen = strlen(binCoorFile)+1;
06839   msg->put(filelen);
06840   msg->put(filelen, binCoorFile);
06841 
06842   if(binVelFile) {
06843     filelen = strlen(binVelFile)+1;
06844     msg->put(filelen);
06845     msg->put(filelen, binVelFile);
06846   }
06847 
06848   if(binRefFile) {
06849     filelen = strlen(binRefFile)+1;
06850     msg->put(filelen);
06851     msg->put(filelen, binRefFile);
06852   }
06853 #endif
06854 
06855   mgridforcelist.pack_data(msg);
06856   
06857   msg->end();
06858 }


Member Data Documentation

int SimParameters::aaAngleExp

Definition at line 898 of file SimParameters.h.

BigReal SimParameters::accelMDalpha

Definition at line 574 of file SimParameters.h.

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

Bool SimParameters::accelMDDebugOn

Definition at line 569 of file SimParameters.h.

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

Bool SimParameters::accelMDdihe

Definition at line 567 of file SimParameters.h.

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

Bool SimParameters::accelMDdual

Definition at line 568 of file SimParameters.h.

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

BigReal SimParameters::accelMDE

Definition at line 573 of file SimParameters.h.

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

BigReal SimParameters::accelMDFirstStep

Definition at line 570 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDG

Definition at line 578 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDPrepSteps

Definition at line 582 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDSteps

Definition at line 580 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiPrepSteps

Definition at line 583 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiSteps

Definition at line 581 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGiE

Definition at line 579 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGresetVaftercmd

Definition at line 588 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGRestart

Definition at line 586 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

char SimParameters::accelMDGRestartFile[128]

Definition at line 587 of file SimParameters.h.

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

BigReal SimParameters::accelMDGSigma0D

Definition at line 585 of file SimParameters.h.

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

BigReal SimParameters::accelMDGSigma0P

Definition at line 584 of file SimParameters.h.

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

BigReal SimParameters::accelMDLastStep

Definition at line 571 of file SimParameters.h.

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

Bool SimParameters::accelMDOn

Definition at line 566 of file SimParameters.h.

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

int SimParameters::accelMDOutFreq

Definition at line 572 of file SimParameters.h.

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

BigReal SimParameters::accelMDTalpha

Definition at line 576 of file SimParameters.h.

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

BigReal SimParameters::accelMDTE

Definition at line 575 of file SimParameters.h.

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

BigReal SimParameters::adaptTempAutoDt

Definition at line 599 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempBins

Definition at line 600 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempCgamma

Definition at line 602 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempDebug

Definition at line 592 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

BigReal SimParameters::adaptTempDt

Definition at line 601 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempFirstStep

Definition at line 593 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

int SimParameters::adaptTempFreq

Definition at line 596 of file SimParameters.h.

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

char SimParameters::adaptTempInFile[128]

Definition at line 605 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempLangevin

Definition at line 603 of file SimParameters.h.

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

int SimParameters::adaptTempLastStep

Definition at line 594 of file SimParameters.h.

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

Bool SimParameters::adaptTempOn

Definition at line 591 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and Controller::rescaleVelocities().

int SimParameters::adaptTempOutFreq

Definition at line 595 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRandom

Definition at line 608 of file SimParameters.h.

Bool SimParameters::adaptTempRescale

Definition at line 604 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

char SimParameters::adaptTempRestartFile[128]

Definition at line 606 of file SimParameters.h.

int SimParameters::adaptTempRestartFreq

Definition at line 607 of file SimParameters.h.

Referenced by Controller::adaptTempWriteRestart().

BigReal SimParameters::adaptTempTmax

Definition at line 598 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempTmin

Definition at line 597 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::alchBondDecouple

Definition at line 420 of file SimParameters.h.

BigReal SimParameters::alchBondLambdaEnd

Definition at line 414 of file SimParameters.h.

Bool SimParameters::alchDecouple

Definition at line 419 of file SimParameters.h.

BigReal SimParameters::alchDispLambda

Definition at line 391 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambda

Definition at line 392 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambdaStart

Definition at line 403 of file SimParameters.h.

Bool SimParameters::alchEnsembleAvg

Definition at line 398 of file SimParameters.h.

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

int SimParameters::alchEquilSteps

Definition at line 400 of file SimParameters.h.

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

Bool SimParameters::alchFepElecOn

Definition at line 381 of file SimParameters.h.

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

Bool SimParameters::alchFepOn

Definition at line 377 of file SimParameters.h.

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

Bool SimParameters::alchFepWCADispOn

Definition at line 380 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut1

Definition at line 393 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut2

Definition at line 394 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut3

Definition at line 395 of file SimParameters.h.

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

Bool SimParameters::alchFepWCARepuOn

Definition at line 379 of file SimParameters.h.

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

Bool SimParameters::alchFepWhamOn

Definition at line 382 of file SimParameters.h.

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

BigReal SimParameters::alchLambda

Definition at line 384 of file SimParameters.h.

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

BigReal SimParameters::alchLambda2

Definition at line 385 of file SimParameters.h.

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

int SimParameters::alchLambdaFreq

Definition at line 386 of file SimParameters.h.

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

int SimParameters::alchMethod

Definition at line 383 of file SimParameters.h.

Bool SimParameters::alchOn

Definition at line 376 of file SimParameters.h.

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

Bool SimParameters::alchOnAtStartup

Definition at line 375 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::alchOutFile[128]

Definition at line 399 of file SimParameters.h.

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

int SimParameters::alchOutFreq

Definition at line 397 of file SimParameters.h.

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

BigReal SimParameters::alchRepLambda

Definition at line 390 of file SimParameters.h.

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

BigReal SimParameters::alchTemp

Definition at line 396 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOn

Definition at line 378 of file SimParameters.h.

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

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 409 of file SimParameters.h.

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 401 of file SimParameters.h.

BigReal SimParameters::alpha_cutoff

Definition at line 500 of file SimParameters.h.

BigReal SimParameters::alpha_max

Definition at line 501 of file SimParameters.h.

Bool SimParameters::amberOn

Definition at line 919 of file SimParameters.h.

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

char SimParameters::auxFilename[128]

Definition at line 200 of file SimParameters.h.

Referenced by CollectionMaster::receiveDataStream().

Bool SimParameters::benchTimestep

Definition at line 156 of file SimParameters.h.

BigReal SimParameters::berendsenPressureCompressibility

Definition at line 632 of file SimParameters.h.

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

int SimParameters::berendsenPressureFreq

Definition at line 634 of file SimParameters.h.

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

Bool SimParameters::berendsenPressureOn

Definition at line 630 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 633 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureTarget

Definition at line 631 of file SimParameters.h.

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

Bool SimParameters::binaryOutput

Definition at line 217 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

Bool SimParameters::binaryRestart

Definition at line 215 of file SimParameters.h.

char* SimParameters::binAtomFile

Definition at line 957 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binCoorFile

Definition at line 958 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binRefFile

Definition at line 960 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binVelFile

Definition at line 959 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

int SimParameters::bondedCUDA

Definition at line 743 of file SimParameters.h.

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

zVector SimParameters::cellBasisVector1

Definition at line 116 of file SimParameters.h.

Referenced by readExtendedSystem().

zVector SimParameters::cellBasisVector2

Definition at line 117 of file SimParameters.h.

Referenced by readExtendedSystem().

zVector SimParameters::cellBasisVector3

Definition at line 118 of file SimParameters.h.

Referenced by readExtendedSystem().

zVector SimParameters::cellOrigin

Definition at line 119 of file SimParameters.h.

Referenced by readExtendedSystem().

Bool SimParameters::COLDOn

Definition at line 554 of file SimParameters.h.

BigReal SimParameters::COLDRate

Definition at line 556 of file SimParameters.h.

BigReal SimParameters::COLDTemp

Definition at line 557 of file SimParameters.h.

Bool SimParameters::colvarsOn

Definition at line 531 of file SimParameters.h.

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

Bool SimParameters::commOnly

Definition at line 858 of file SimParameters.h.

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

Bool SimParameters::comMove

Definition at line 178 of file SimParameters.h.

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

char SimParameters::computeMapFilename[128]

Definition at line 966 of file SimParameters.h.

char SimParameters::consForceFile[128]

Definition at line 810 of file SimParameters.h.

Bool SimParameters::consForceOn

Definition at line 809 of file SimParameters.h.

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

BigReal SimParameters::consForceScaling

Definition at line 811 of file SimParameters.h.

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

char SimParameters::consTorqueAxisFile[128]

Definition at line 331 of file SimParameters.h.

char SimParameters::consTorqueFile[128]

Definition at line 329 of file SimParameters.h.

BigReal SimParameters::consTorqueGlobVal

Definition at line 333 of file SimParameters.h.

Bool SimParameters::consTorqueOn

Definition at line 328 of file SimParameters.h.

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

char SimParameters::consTorquePivotFile[128]

Definition at line 332 of file SimParameters.h.

char SimParameters::consTorqueValFile[128]

Definition at line 334 of file SimParameters.h.

int SimParameters::constraintExp

Definition at line 252 of file SimParameters.h.

BigReal SimParameters::constraintScaling

Definition at line 280 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::constraintsOn

Definition at line 250 of file SimParameters.h.

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

Bool SimParameters::constrXOn

Definition at line 271 of file SimParameters.h.

Bool SimParameters::constrYOn

Definition at line 271 of file SimParameters.h.

Bool SimParameters::constrZOn

Definition at line 271 of file SimParameters.h.

Bool SimParameters::cosAngles

Definition at line 520 of file SimParameters.h.

BigReal SimParameters::coulomb_radius_offset

Definition at line 494 of file SimParameters.h.

BigReal SimParameters::cutoff

Definition at line 219 of file SimParameters.h.

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

char SimParameters::cylindricalBCAxis

Definition at line 782 of file SimParameters.h.

int SimParameters::cylindricalBCexp1

Definition at line 787 of file SimParameters.h.

int SimParameters::cylindricalBCexp2

Definition at line 788 of file SimParameters.h.

BigReal SimParameters::cylindricalBCk1

Definition at line 789 of file SimParameters.h.

BigReal SimParameters::cylindricalBCk2

Definition at line 790 of file SimParameters.h.

BigReal SimParameters::cylindricalBCl1

Definition at line 785 of file SimParameters.h.

BigReal SimParameters::cylindricalBCl2

Definition at line 786 of file SimParameters.h.

Bool SimParameters::cylindricalBCOn

Definition at line 779 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::cylindricalBCr1

Definition at line 783 of file SimParameters.h.

BigReal SimParameters::cylindricalBCr2

Definition at line 784 of file SimParameters.h.

zVector SimParameters::cylindricalCenter

Definition at line 781 of file SimParameters.h.

BigReal SimParameters::daCutoffDist

Definition at line 905 of file SimParameters.h.

BigReal SimParameters::daOffDist

Definition at line 905 of file SimParameters.h.

BigReal SimParameters::daOnDist

Definition at line 905 of file SimParameters.h.

char SimParameters::dcdFilename[128]

Definition at line 201 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::dcdFrequency

Definition at line 191 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::dcdUnitCell

Definition at line 193 of file SimParameters.h.

BigReal SimParameters::dhaCutoffAngle

Definition at line 901 of file SimParameters.h.

BigReal SimParameters::dhaOffAngle

Definition at line 901 of file SimParameters.h.

BigReal SimParameters::dhaOnAngle

Definition at line 901 of file SimParameters.h.

BigReal SimParameters::dielectric

Definition at line 185 of file SimParameters.h.

Bool SimParameters::dihedralOn

Definition at line 553 of file SimParameters.h.

Bool SimParameters::disableTopology

Definition at line 153 of file SimParameters.h.

int SimParameters::distAttExp

Definition at line 898 of file SimParameters.h.

int SimParameters::distRepExp

Definition at line 898 of file SimParameters.h.

BigReal SimParameters::drudeBondConst

Definition at line 512 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::drudeBondLen

Definition at line 510 of file SimParameters.h.

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

BigReal SimParameters::drudeDamping

Definition at line 508 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::drudeHardWallOn

Definition at line 506 of file SimParameters.h.

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

BigReal SimParameters::drudeNbtholeCut

Definition at line 513 of file SimParameters.h.

Bool SimParameters::drudeOn

Definition at line 505 of file SimParameters.h.

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

BigReal SimParameters::drudeTemp

Definition at line 507 of file SimParameters.h.

Referenced by Sequencer::langevinVelocitiesBBK2().

BigReal SimParameters::dt

Definition at line 112 of file SimParameters.h.

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

zVector SimParameters::eField

Definition at line 794 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::eFieldFreq

Definition at line 795 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::eFieldNormalized

Definition at line 793 of file SimParameters.h.

Bool SimParameters::eFieldOn

Definition at line 792 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::eFieldPhase

Definition at line 796 of file SimParameters.h.

Referenced by scriptSet().

ExclusionSettings SimParameters::exclude

Definition at line 186 of file SimParameters.h.

Referenced by buildExclusions().

Bool SimParameters::excludeFromPressure

Definition at line 619 of file SimParameters.h.

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

char SimParameters::extCoordFilename[128]

Definition at line 431 of file SimParameters.h.

char SimParameters::extForceFilename[128]

Definition at line 432 of file SimParameters.h.

char SimParameters::extForcesCommand[256]

Definition at line 430 of file SimParameters.h.

Bool SimParameters::extForcesOn

Definition at line 429 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::extraBondsOn

Definition at line 807 of file SimParameters.h.

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

Bool SimParameters::FFTWEstimate

Definition at line 748 of file SimParameters.h.

Bool SimParameters::FFTWPatient

Definition at line 749 of file SimParameters.h.

Bool SimParameters::FFTWUseWisdom

Definition at line 750 of file SimParameters.h.

char SimParameters::FFTWWisdomFile[128]

Definition at line 751 of file SimParameters.h.

char* SimParameters::FFTWWisdomString

Definition at line 752 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

int SimParameters::firstLdbStep

Definition at line 130 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::firstTimestep

Definition at line 830 of file SimParameters.h.

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

Bool SimParameters::fixCellDims

Definition at line 625 of file SimParameters.h.

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

Bool SimParameters::fixCellDimX

Definition at line 626 of file SimParameters.h.

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

Bool SimParameters::fixCellDimY

Definition at line 627 of file SimParameters.h.

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

Bool SimParameters::fixCellDimZ

Definition at line 628 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsForceOutput

Definition at line 535 of file SimParameters.h.

Bool SimParameters::fixedAtomsForces

Definition at line 534 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsOn

Definition at line 533 of file SimParameters.h.

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

int SimParameters::FMAFFTBlock

Definition at line 672 of file SimParameters.h.

Bool SimParameters::FMAFFTOn

Definition at line 671 of file SimParameters.h.

int SimParameters::FMALevels

Definition at line 669 of file SimParameters.h.

int SimParameters::FMAMp

Definition at line 670 of file SimParameters.h.

Bool SimParameters::FMAOn

Definition at line 668 of file SimParameters.h.

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

BigReal SimParameters::fmaTheta

Definition at line 126 of file SimParameters.h.

int SimParameters::FMMLevels

Definition at line 716 of file SimParameters.h.

Bool SimParameters::FMMOn

Definition at line 715 of file SimParameters.h.

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

BigReal SimParameters::FMMPadding

Definition at line 717 of file SimParameters.h.

char SimParameters::forceDcdFilename[128]

Definition at line 203 of file SimParameters.h.

int SimParameters::forceDcdFrequency

Definition at line 196 of file SimParameters.h.

Bool SimParameters::freeEnergyOn

Definition at line 529 of file SimParameters.h.

Referenced by ParallelIOMgr::freeMolSpace().

BigReal SimParameters::fsMax

Definition at line 491 of file SimParameters.h.

Bool SimParameters::fullDirectOn

Definition at line 674 of file SimParameters.h.

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

int SimParameters::fullElectFrequency

Definition at line 124 of file SimParameters.h.

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

BigReal SimParameters::gbis_beta

Definition at line 498 of file SimParameters.h.

BigReal SimParameters::gbis_delta

Definition at line 497 of file SimParameters.h.

BigReal SimParameters::gbis_gamma

Definition at line 499 of file SimParameters.h.

Bool SimParameters::GBISOn

Definition at line 490 of file SimParameters.h.

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

Bool SimParameters::GBISserOn

Definition at line 492 of file SimParameters.h.

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

Bool SimParameters::genCompressedPsf

Definition at line 941 of file SimParameters.h.

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

Bool SimParameters::globalForcesOn

Definition at line 521 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::globalOn

Definition at line 552 of file SimParameters.h.

char SimParameters::goCoordinates[128]

Definition at line 291 of file SimParameters.h.

Bool SimParameters::goForcesOn

Definition at line 289 of file SimParameters.h.

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

Bool SimParameters::goGroPair

Definition at line 288 of file SimParameters.h.

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

GoChoices SimParameters::goMethod

Definition at line 293 of file SimParameters.h.

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

char SimParameters::goParameters[128]

Definition at line 290 of file SimParameters.h.

Bool SimParameters::gridforcechecksize

Definition at line 263 of file SimParameters.h.

Bool SimParameters::gridforceContA1

Definition at line 258 of file SimParameters.h.

Bool SimParameters::gridforceContA2

Definition at line 259 of file SimParameters.h.

Bool SimParameters::gridforceContA3

Definition at line 260 of file SimParameters.h.

Bool SimParameters::gridforceLite

Definition at line 262 of file SimParameters.h.

Bool SimParameters::gridforceOn

Definition at line 255 of file SimParameters.h.

zVector SimParameters::gridforceScale

Definition at line 257 of file SimParameters.h.

zVector SimParameters::gridforceVOffset

Definition at line 261 of file SimParameters.h.

Bool SimParameters::gridforceVolts

Definition at line 256 of file SimParameters.h.

Bool SimParameters::gromacsOn

Definition at line 924 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::haAngleExp

Definition at line 898 of file SimParameters.h.

BigReal SimParameters::hgroupCutoff

Definition at line 842 of file SimParameters.h.

int SimParameters::hybridGroupSize

Definition at line 134 of file SimParameters.h.

Bool SimParameters::HydrogenBonds

Definition at line 888 of file SimParameters.h.

Bool SimParameters::ignoreMass

Definition at line 839 of file SimParameters.h.

int SimParameters::IMDfreq

Definition at line 910 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::IMDignore

Definition at line 913 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDignoreForces

Definition at line 915 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDon

Definition at line 908 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::IMDport

Definition at line 909 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDwait

Definition at line 911 of file SimParameters.h.

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

BigReal SimParameters::initialTemp

Definition at line 176 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Controller::algorithm(), WorkDistrib::createAtomLists(), Sequencer::integrate(), Sequencer::reinitVelocities(), and scriptSet().

BigReal SimParameters::ion_concentration

Definition at line 496 of file SimParameters.h.

BigReal SimParameters::kappa

Definition at line 495 of file SimParameters.h.

Bool SimParameters::langevin_useBAOAB

Definition at line 542 of file SimParameters.h.

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

BigReal SimParameters::langevinDamping

Definition at line 540 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinHydrogen

Definition at line 541 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinOn

Definition at line 538 of file SimParameters.h.

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

Bool SimParameters::langevinOnAtStartup

Definition at line 537 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::langevinPistonBarrier

Definition at line 637 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

BigReal SimParameters::langevinPistonDecay

Definition at line 640 of file SimParameters.h.

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

Bool SimParameters::langevinPistonOn

Definition at line 636 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonPeriod

Definition at line 639 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTarget

Definition at line 638 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTemp

Definition at line 641 of file SimParameters.h.

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

BigReal SimParameters::langevinTemp

Definition at line 539 of file SimParameters.h.

Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and scriptSet().

int SimParameters::lastLdbStep

Definition at line 132 of file SimParameters.h.

Lattice SimParameters::lattice

Definition at line 120 of file SimParameters.h.

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

Bool SimParameters::LCPOOn

Definition at line 502 of file SimParameters.h.

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

int SimParameters::ldBalancer

Definition at line 127 of file SimParameters.h.

BigReal SimParameters::ldbBackgroundScaling

Definition at line 135 of file SimParameters.h.

BigReal SimParameters::ldbHomeBackgroundScaling

Definition at line 137 of file SimParameters.h.

int SimParameters::ldbPeriod

Definition at line 129 of file SimParameters.h.

BigReal SimParameters::ldbPMEBackgroundScaling

Definition at line 136 of file SimParameters.h.

BigReal SimParameters::ldbRelativeGrainsize

Definition at line 138 of file SimParameters.h.

int SimParameters::ldbStrategy

Definition at line 128 of file SimParameters.h.

Bool SimParameters::ldbUnloadOne

Definition at line 170 of file SimParameters.h.

Bool SimParameters::ldbUnloadOutputPEs

Definition at line 171 of file SimParameters.h.

Bool SimParameters::ldbUnloadPME

Definition at line 168 of file SimParameters.h.

Bool SimParameters::ldbUnloadZero

Definition at line 169 of file SimParameters.h.

int SimParameters::lesFactor

Definition at line 425 of file SimParameters.h.

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

Bool SimParameters::lesOn

Definition at line 424 of file SimParameters.h.

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

Bool SimParameters::lesReduceMass

Definition at line 427 of file SimParameters.h.

Bool SimParameters::lesReduceTemp

Definition at line 426 of file SimParameters.h.

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

BigReal SimParameters::limitDist

Definition at line 226 of file SimParameters.h.

Bool SimParameters::LJcorrection

Definition at line 111 of file SimParameters.h.

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

Bool SimParameters::loadComputeMap

Definition at line 968 of file SimParameters.h.

Bool SimParameters::lonepairs

Definition at line 108 of file SimParameters.h.

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

int SimParameters::longSplitting

Definition at line 836 of file SimParameters.h.

BigReal SimParameters::loweAndersenCutoff

Definition at line 549 of file SimParameters.h.

Bool SimParameters::loweAndersenOn

Definition at line 546 of file SimParameters.h.

Referenced by Sequencer::integrate().

BigReal SimParameters::loweAndersenRate

Definition at line 548 of file SimParameters.h.

BigReal SimParameters::loweAndersenTemp

Definition at line 547 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::mallocTest

Definition at line 945 of file SimParameters.h.

Referenced by Node::startup().

BigReal SimParameters::margin

Definition at line 220 of file SimParameters.h.

Bool SimParameters::martiniDielAllow

Definition at line 236 of file SimParameters.h.

Bool SimParameters::martiniSwitching

Definition at line 234 of file SimParameters.h.

int SimParameters::maxExclusionFlags

Definition at line 876 of file SimParameters.h.

BigReal SimParameters::maximumMove

Definition at line 764 of file SimParameters.h.

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

int SimParameters::maxPairPart

Definition at line 864 of file SimParameters.h.

int SimParameters::maxPatches

Definition at line 167 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::maxSelfPart

Definition at line 862 of file SimParameters.h.

Bool SimParameters::mergeCrossterms

Definition at line 828 of file SimParameters.h.

Referenced by Controller::printEnergies().

MGridforceParamsList SimParameters::mgridforcelist

Definition at line 266 of file SimParameters.h.

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

Bool SimParameters::mgridforceOn

Definition at line 265 of file SimParameters.h.

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

int SimParameters::mic_deviceThreshold

Definition at line 976 of file SimParameters.h.

int SimParameters::mic_hostSplit

Definition at line 971 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p1

Definition at line 973 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p2

Definition at line 974 of file SimParameters.h.

int SimParameters::mic_numParts_self_p1

Definition at line 972 of file SimParameters.h.

int SimParameters::mic_singleKernel

Definition at line 977 of file SimParameters.h.

int SimParameters::mic_unloadMICPEs

Definition at line 975 of file SimParameters.h.

int SimParameters::minAtomsPerPatch

Definition at line 874 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

BigReal SimParameters::minBabyStep

Definition at line 761 of file SimParameters.h.

Bool SimParameters::minimizeCGOn

Definition at line 758 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::minimizeOn

Definition at line 763 of file SimParameters.h.

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

BigReal SimParameters::minLineGoal

Definition at line 762 of file SimParameters.h.

Referenced by Controller::minimize().

BigReal SimParameters::minTinyStep

Definition at line 760 of file SimParameters.h.

Bool SimParameters::minVerbose

Definition at line 759 of file SimParameters.h.

Referenced by Controller::minimize().

Bool SimParameters::miscForcesOn

Definition at line 530 of file SimParameters.h.

int SimParameters::mollyIter

Definition at line 846 of file SimParameters.h.

int SimParameters::mollyOn

Definition at line 844 of file SimParameters.h.

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

BigReal SimParameters::mollyTol

Definition at line 845 of file SimParameters.h.

char SimParameters::movDragFile[128]

Definition at line 311 of file SimParameters.h.

BigReal SimParameters::movDragGlobVel

Definition at line 313 of file SimParameters.h.

Referenced by Sequencer::addMovDragToPosition().

Bool SimParameters::movDragOn

Definition at line 310 of file SimParameters.h.

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

char SimParameters::movDragVelFile[128]

Definition at line 314 of file SimParameters.h.

Bool SimParameters::movingConstraintsOn

Definition at line 297 of file SimParameters.h.

zVector SimParameters::movingConsVel

Definition at line 299 of file SimParameters.h.

int SimParameters::MSMApprox

Definition at line 684 of file SimParameters.h.

int SimParameters::MSMBlockSizeX

Definition at line 694 of file SimParameters.h.

int SimParameters::MSMBlockSizeY

Definition at line 695 of file SimParameters.h.

int SimParameters::MSMBlockSizeZ

Definition at line 696 of file SimParameters.h.

BigReal SimParameters::MSMGridSpacing

Definition at line 698 of file SimParameters.h.

int SimParameters::MSMLevels

Definition at line 690 of file SimParameters.h.

Bool SimParameters::MSMOn

Definition at line 677 of file SimParameters.h.

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

BigReal SimParameters::MSMPadding

Definition at line 700 of file SimParameters.h.

int SimParameters::MSMQuality

Definition at line 680 of file SimParameters.h.

Bool SimParameters::MsmSerialOn

Definition at line 713 of file SimParameters.h.

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

int SimParameters::MSMSplit

Definition at line 687 of file SimParameters.h.

BigReal SimParameters::MSMxmax

Definition at line 707 of file SimParameters.h.

BigReal SimParameters::MSMxmin

Definition at line 706 of file SimParameters.h.

BigReal SimParameters::MSMymax

Definition at line 709 of file SimParameters.h.

BigReal SimParameters::MSMymin

Definition at line 708 of file SimParameters.h.

BigReal SimParameters::MSMzmax

Definition at line 711 of file SimParameters.h.

BigReal SimParameters::MSMzmin

Definition at line 710 of file SimParameters.h.

MTSChoices SimParameters::MTSAlgorithm

Definition at line 833 of file SimParameters.h.

Referenced by Sequencer::integrate().

int SimParameters::multigratorNoseHooverChainLength

Definition at line 650 of file SimParameters.h.

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

Bool SimParameters::multigratorOn

Definition at line 643 of file SimParameters.h.

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

int SimParameters::multigratorPressureFreq

Definition at line 646 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureRelaxationTime

Definition at line 645 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureTarget

Definition at line 644 of file SimParameters.h.

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

int SimParameters::multigratorTemperatureFreq

Definition at line 649 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureRelaxationTime

Definition at line 648 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureTarget

Definition at line 647 of file SimParameters.h.

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

int SimParameters::N

Definition at line 113 of file SimParameters.h.

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

int SimParameters::nonbondedFrequency

Definition at line 122 of file SimParameters.h.

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

BigReal SimParameters::nonbondedScaling

Definition at line 190 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::noPatchesOnOne

Definition at line 174 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnOutputPEs

Definition at line 173 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnZero

Definition at line 172 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::numAtomsPair

Definition at line 870 of file SimParameters.h.

int SimParameters::numAtomsPair2

Definition at line 872 of file SimParameters.h.

int SimParameters::numAtomsSelf

Definition at line 866 of file SimParameters.h.

int SimParameters::numAtomsSelf2

Definition at line 868 of file SimParameters.h.

int SimParameters::numinputprocs

Definition at line 956 of file SimParameters.h.

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

int SimParameters::numoutputprocs

Definition at line 963 of file SimParameters.h.

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

int SimParameters::numoutputwrts

Definition at line 964 of file SimParameters.h.

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

int SimParameters::numTraceSteps

Definition at line 141 of file SimParameters.h.

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

int SimParameters::outputCudaTiming

Definition at line 822 of file SimParameters.h.

int SimParameters::outputEnergies

Definition at line 813 of file SimParameters.h.

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

char SimParameters::outputFilename[128]

Definition at line 205 of file SimParameters.h.

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

Bool SimParameters::outputMaps

Definition at line 149 of file SimParameters.h.

Referenced by Node::outputPatchComputeMaps().

int SimParameters::outputMomenta

Definition at line 816 of file SimParameters.h.

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

int SimParameters::outputPairlists

Definition at line 248 of file SimParameters.h.

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

Bool SimParameters::outputPatchDetails

Definition at line 878 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

int SimParameters::outputPressure

Definition at line 825 of file SimParameters.h.

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

int SimParameters::outputTiming

Definition at line 819 of file SimParameters.h.

Referenced by Controller::printTiming().

int SimParameters::pairInteractionGroup1

Definition at line 516 of file SimParameters.h.

int SimParameters::pairInteractionGroup2

Definition at line 517 of file SimParameters.h.

Bool SimParameters::pairInteractionOn

Definition at line 515 of file SimParameters.h.

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

Bool SimParameters::pairInteractionSelf

Definition at line 518 of file SimParameters.h.

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

BigReal SimParameters::pairlistDist

Definition at line 238 of file SimParameters.h.

BigReal SimParameters::pairlistGrow

Definition at line 246 of file SimParameters.h.

int SimParameters::pairlistMinProcs

Definition at line 240 of file SimParameters.h.

BigReal SimParameters::pairlistShrink

Definition at line 245 of file SimParameters.h.

int SimParameters::pairlistsPerCycle

Definition at line 244 of file SimParameters.h.

Referenced by Sequencer::runComputeObjects().

BigReal SimParameters::pairlistTrigger

Definition at line 247 of file SimParameters.h.

Bool SimParameters::paraTypeCharmmOn

Definition at line 284 of file SimParameters.h.

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

Bool SimParameters::paraTypeXplorOn

Definition at line 283 of file SimParameters.h.

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

BigReal SimParameters::patchDimension

Definition at line 221 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::PMEBarrier

Definition at line 730 of file SimParameters.h.

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 721 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::PMEGridSizeX

Definition at line 723 of file SimParameters.h.

int SimParameters::PMEGridSizeY

Definition at line 724 of file SimParameters.h.

int SimParameters::PMEGridSizeZ

Definition at line 725 of file SimParameters.h.

BigReal SimParameters::PMEGridSpacing

Definition at line 726 of file SimParameters.h.

int SimParameters::PMEInterpOrder

Definition at line 722 of file SimParameters.h.

int SimParameters::PMEMinPoints

Definition at line 729 of file SimParameters.h.

int SimParameters::PMEMinSlices

Definition at line 728 of file SimParameters.h.

Bool SimParameters::PMEOffload

Definition at line 738 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA().

Bool SimParameters::PMEOn

Definition at line 719 of file SimParameters.h.

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

int SimParameters::PMEPencils

Definition at line 731 of file SimParameters.h.

int SimParameters::PMEPencilsX

Definition at line 732 of file SimParameters.h.

int SimParameters::PMEPencilsXLayout

Definition at line 736 of file SimParameters.h.

int SimParameters::PMEPencilsY

Definition at line 733 of file SimParameters.h.

int SimParameters::PMEPencilsYLayout

Definition at line 735 of file SimParameters.h.

int SimParameters::PMEPencilsZ

Definition at line 734 of file SimParameters.h.

int SimParameters::PMEProcessors

Definition at line 727 of file SimParameters.h.

int SimParameters::PMESendOrder

Definition at line 737 of file SimParameters.h.

BigReal SimParameters::PMETolerance

Definition at line 720 of file SimParameters.h.

int SimParameters::pressureProfileAtomTypes

Definition at line 657 of file SimParameters.h.

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

Bool SimParameters::pressureProfileEwaldOn

Definition at line 658 of file SimParameters.h.

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

int SimParameters::pressureProfileEwaldX

Definition at line 659 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldY

Definition at line 660 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldZ

Definition at line 661 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileFreq

Definition at line 656 of file SimParameters.h.

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

Bool SimParameters::pressureProfileOn

Definition at line 654 of file SimParameters.h.

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

int SimParameters::pressureProfileSlabs

Definition at line 655 of file SimParameters.h.

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

Bool SimParameters::printBadContacts

Definition at line 487 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Bool SimParameters::printExclusions

Definition at line 946 of file SimParameters.h.

int SimParameters::proxyRecvSpanningTree

Definition at line 950 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

int SimParameters::proxySendSpanningTree

Definition at line 949 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

int SimParameters::proxyTreeBranchFactor

Definition at line 952 of file SimParameters.h.

Referenced by Node::startup().

char SimParameters::qmBaseDir[256]

Definition at line 445 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmBondColumn[16]

Definition at line 455 of file SimParameters.h.

Bool SimParameters::qmBondDist

Definition at line 456 of file SimParameters.h.

Bool SimParameters::qmBondOn

Definition at line 454 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmBondScheme

Definition at line 460 of file SimParameters.h.

char SimParameters::qmBondSchemeS[16]

Definition at line 459 of file SimParameters.h.

int SimParameters::qmBondValType

Definition at line 457 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmBondValueTypeS[16]

Definition at line 458 of file SimParameters.h.

Bool SimParameters::qmChrgFromPSF

Definition at line 439 of file SimParameters.h.

int SimParameters::qmChrgMode

Definition at line 443 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmChrgModeS[16]

Definition at line 442 of file SimParameters.h.

char SimParameters::qmColumn[16]

Definition at line 444 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmCSMD

Definition at line 480 of file SimParameters.h.

char SimParameters::qmCSMDFile[128]

Definition at line 481 of file SimParameters.h.

Bool SimParameters::qmCustomPCSel

Definition at line 472 of file SimParameters.h.

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

Bool SimParameters::qmElecEmbed

Definition at line 470 of file SimParameters.h.

int SimParameters::qmEnergyOutFreq

Definition at line 483 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

char SimParameters::qmExecPath[256]

Definition at line 440 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmForcesOn

Definition at line 436 of file SimParameters.h.

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

int SimParameters::qmFormat

Definition at line 450 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmLSSFreq

Definition at line 475 of file SimParameters.h.

int SimParameters::qmLSSMode

Definition at line 478 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmLSSModeS[16]

Definition at line 477 of file SimParameters.h.

Bool SimParameters::qmLSSOn

Definition at line 474 of file SimParameters.h.

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

char SimParameters::qmLSSResname[5]

Definition at line 476 of file SimParameters.h.

Bool SimParameters::qmMOPACAddConfigChrg

Definition at line 452 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmNoPC

Definition at line 469 of file SimParameters.h.

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

int SimParameters::qmOutFreq

Definition at line 484 of file SimParameters.h.

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

char SimParameters::qmParamPDB[128]

Definition at line 437 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::qmParamPDBDefined

Definition at line 438 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::qmPCScheme

Definition at line 465 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSchemeS[16]

Definition at line 464 of file SimParameters.h.

int SimParameters::qmPCSelFreq

Definition at line 471 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmPCSwitchOn

Definition at line 461 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmPCSwitchType

Definition at line 463 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSwitchTypeS[16]

Definition at line 462 of file SimParameters.h.

int SimParameters::qmPosOutFreq

Definition at line 485 of file SimParameters.h.

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

char SimParameters::qmPrepProc[256]

Definition at line 448 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmPrepProcOn

Definition at line 449 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmReplaceAll

Definition at line 451 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::qmSecProc[256]

Definition at line 446 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmSecProcOn

Definition at line 447 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmSimsPerNode

Definition at line 466 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmSoftware[128]

Definition at line 441 of file SimParameters.h.

Bool SimParameters::qmVDW

Definition at line 468 of file SimParameters.h.

unsigned int SimParameters::randomSeed

Definition at line 666 of file SimParameters.h.

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

Bool SimParameters::readExclusions

Definition at line 920 of file SimParameters.h.

Referenced by buildExclusions().

int SimParameters::reassignFreq

Definition at line 611 of file SimParameters.h.

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

BigReal SimParameters::reassignHold

Definition at line 614 of file SimParameters.h.

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

BigReal SimParameters::reassignIncr

Definition at line 613 of file SimParameters.h.

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

BigReal SimParameters::reassignTemp

Definition at line 612 of file SimParameters.h.

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

Bool SimParameters::replicaUniformPatchGrids

Definition at line 880 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::rescaleFreq

Definition at line 563 of file SimParameters.h.

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

BigReal SimParameters::rescaleTemp

Definition at line 564 of file SimParameters.h.

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

char SimParameters::restartFilename[128]

Definition at line 210 of file SimParameters.h.

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

int SimParameters::restartFrequency

Definition at line 211 of file SimParameters.h.

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

Bool SimParameters::restartSave

Definition at line 213 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::restartSaveDcd

Definition at line 214 of file SimParameters.h.

int SimParameters::rigidBonds

Definition at line 848 of file SimParameters.h.

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

int SimParameters::rigidDie

Definition at line 853 of file SimParameters.h.

int SimParameters::rigidIter

Definition at line 852 of file SimParameters.h.

BigReal SimParameters::rigidTol

Definition at line 851 of file SimParameters.h.

zVector SimParameters::rotConsAxis

Definition at line 304 of file SimParameters.h.

zVector SimParameters::rotConsPivot

Definition at line 305 of file SimParameters.h.

Bool SimParameters::rotConstraintsOn

Definition at line 302 of file SimParameters.h.

BigReal SimParameters::rotConsVel

Definition at line 306 of file SimParameters.h.

char SimParameters::rotDragAxisFile[128]

Definition at line 321 of file SimParameters.h.

char SimParameters::rotDragFile[128]

Definition at line 319 of file SimParameters.h.

BigReal SimParameters::rotDragGlobVel

Definition at line 323 of file SimParameters.h.

Referenced by Sequencer::addRotDragToPosition().

Bool SimParameters::rotDragOn

Definition at line 318 of file SimParameters.h.

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

char SimParameters::rotDragPivotFile[128]

Definition at line 322 of file SimParameters.h.

char SimParameters::rotDragVelFile[128]

Definition at line 324 of file SimParameters.h.

BigReal SimParameters::scale14

Definition at line 188 of file SimParameters.h.

BigReal SimParameters::scriptArg1

Definition at line 930 of file SimParameters.h.

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

BigReal SimParameters::scriptArg2

Definition at line 931 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg3

Definition at line 932 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg4

Definition at line 933 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg5

Definition at line 934 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::scriptIntArg1

Definition at line 935 of file SimParameters.h.

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

int SimParameters::scriptIntArg2

Definition at line 936 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::scriptStringArg1[128]

Definition at line 937 of file SimParameters.h.

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

char SimParameters::scriptStringArg2[128]

Definition at line 938 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::selectConstraintsOn

Definition at line 269 of file SimParameters.h.

int SimParameters::simulatedNodeSize

Definition at line 152 of file SimParameters.h.

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

int SimParameters::simulatedPEs

Definition at line 151 of file SimParameters.h.

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

Bool SimParameters::simulateInitialMapping

Definition at line 150 of file SimParameters.h.

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

zVector SimParameters::SMDDir

Definition at line 341 of file SimParameters.h.

char SimParameters::SMDFile[128]

Definition at line 344 of file SimParameters.h.

BigReal SimParameters::SMDk

Definition at line 342 of file SimParameters.h.

BigReal SimParameters::SMDk2

Definition at line 343 of file SimParameters.h.

Bool SimParameters::SMDOn

Definition at line 339 of file SimParameters.h.

int SimParameters::SMDOutputFreq

Definition at line 345 of file SimParameters.h.

BigReal SimParameters::SMDVel

Definition at line 340 of file SimParameters.h.

BigReal SimParameters::solvent_dielectric

Definition at line 493 of file SimParameters.h.

int SimParameters::sphericalBCexp1

Definition at line 776 of file SimParameters.h.

int SimParameters::sphericalBCexp2

Definition at line 777 of file SimParameters.h.

BigReal SimParameters::sphericalBCk1

Definition at line 770 of file SimParameters.h.

BigReal SimParameters::sphericalBCk2

Definition at line 772 of file SimParameters.h.

Bool SimParameters::sphericalBCOn

Definition at line 767 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::sphericalBCr1

Definition at line 774 of file SimParameters.h.

BigReal SimParameters::sphericalBCr2

Definition at line 775 of file SimParameters.h.

zVector SimParameters::sphericalCenter

Definition at line 769 of file SimParameters.h.

Bool SimParameters::sphericalConstraintsOn

Definition at line 277 of file SimParameters.h.

zVector SimParameters::sphericalConstrCenter

Definition at line 278 of file SimParameters.h.

int SimParameters::splitPatch

Definition at line 841 of file SimParameters.h.

Bool SimParameters::staticAtomAssignment

Definition at line 879 of file SimParameters.h.

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

Bool SimParameters::statsOn

Definition at line 859 of file SimParameters.h.

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

int SimParameters::stepsPerCycle

Definition at line 114 of file SimParameters.h.

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

zVector SimParameters::stirAxis

Definition at line 804 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::stirFilename[128]

Definition at line 799 of file SimParameters.h.

BigReal SimParameters::stirK

Definition at line 803 of file SimParameters.h.

Bool SimParameters::stirOn

Definition at line 798 of file SimParameters.h.

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

zVector SimParameters::stirPivot

Definition at line 805 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::stirStartingTheta

Definition at line 801 of file SimParameters.h.

BigReal SimParameters::stirVel

Definition at line 802 of file SimParameters.h.

Bool SimParameters::storeComputeMap

Definition at line 967 of file SimParameters.h.

zVector SimParameters::strainRate

Definition at line 663 of file SimParameters.h.

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

zVector SimParameters::strainRate2

Definition at line 664 of file SimParameters.h.

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

BigReal SimParameters::surface_tension

Definition at line 503 of file SimParameters.h.

BigReal SimParameters::surfaceTensionTarget

Definition at line 652 of file SimParameters.h.

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

Bool SimParameters::switchingActive

Definition at line 228 of file SimParameters.h.

BigReal SimParameters::switchingDist

Definition at line 232 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::symmetryFile[128]

Definition at line 369 of file SimParameters.h.

int SimParameters::symmetryFirstFullStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryFirstStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

BigReal SimParameters::symmetryk

Definition at line 367 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetrykfile[128]

Definition at line 368 of file SimParameters.h.

int SimParameters::symmetryLastFullStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

int SimParameters::symmetryLastStep

Definition at line 371 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::symmetryMatrixFile[128]

Definition at line 370 of file SimParameters.h.

Bool SimParameters::symmetryOn

Definition at line 366 of file SimParameters.h.

Bool SimParameters::symmetryScaleForces

Definition at line 366 of file SimParameters.h.

Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().

char SimParameters::tableInterpType[128]

Definition at line 352 of file SimParameters.h.

BigReal SimParameters::tableMaxDist

Definition at line 354 of file SimParameters.h.

int SimParameters::tableNumTypes

Definition at line 350 of file SimParameters.h.

Real SimParameters::tableSpacing

Definition at line 353 of file SimParameters.h.

Bool SimParameters::tabulatedEnergies

Definition at line 349 of file SimParameters.h.

char SimParameters::tabulatedEnergiesFile[128]

Definition at line 351 of file SimParameters.h.

char SimParameters::tclBCArgs[128]

Definition at line 528 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::tclBCOn

Definition at line 526 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

char* SimParameters::tclBCScript

Definition at line 527 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Bool SimParameters::tclForcesOn

Definition at line 522 of file SimParameters.h.

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

Bool SimParameters::tclIsThreaded

Definition at line 524 of file SimParameters.h.

Bool SimParameters::tCoupleOn

Definition at line 559 of file SimParameters.h.

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

BigReal SimParameters::tCoupleTemp

Definition at line 561 of file SimParameters.h.

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

Bool SimParameters::testOn

Definition at line 857 of file SimParameters.h.

Bool SimParameters::TMDDiffRMSD

Definition at line 358 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile[128]

Definition at line 360 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

char SimParameters::TMDFile2[128]

Definition at line 360 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDFinalRMSD

Definition at line 363 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDFirstStep

Definition at line 362 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDInitialRMSD

Definition at line 363 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

BigReal SimParameters::TMDk

Definition at line 359 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::TMDLastStep

Definition at line 362 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

Bool SimParameters::TMDOn

Definition at line 358 of file SimParameters.h.

int SimParameters::TMDOutputFreq

Definition at line 361 of file SimParameters.h.

Referenced by GlobalMasterTMD::GlobalMasterTMD().

int SimParameters::totalAtoms

Definition at line 861 of file SimParameters.h.

int SimParameters::traceStartStep

Definition at line 140 of file SimParameters.h.

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

int SimParameters::twoAwayX

Definition at line 164 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayY

Definition at line 165 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::twoAwayZ

Definition at line 166 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::useAntecedent

Definition at line 891 of file SimParameters.h.

int SimParameters::useCkLoop

Definition at line 162 of file SimParameters.h.

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

Bool SimParameters::useCompressedPsf

Definition at line 940 of file SimParameters.h.

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

Bool SimParameters::useConstantArea

Definition at line 622 of file SimParameters.h.

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

Bool SimParameters::useConstantRatio

Definition at line 623 of file SimParameters.h.

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

Bool SimParameters::useCUDA2

Definition at line 742 of file SimParameters.h.

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

Bool SimParameters::useDPME

Definition at line 740 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::useFlexibleCell

Definition at line 621 of file SimParameters.h.

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

Bool SimParameters::useGroupPressure

Definition at line 616 of file SimParameters.h.

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

Bool SimParameters::useManyToMany

Definition at line 745 of file SimParameters.h.

Bool SimParameters::useOptPME

Definition at line 744 of file SimParameters.h.

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

int SimParameters::usePairlists

Definition at line 242 of file SimParameters.h.

Bool SimParameters::usePluginIO

Definition at line 943 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::usePMECUDA

Definition at line 741 of file SimParameters.h.

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

Bool SimParameters::useSettle

Definition at line 855 of file SimParameters.h.

Bool SimParameters::vdwForceSwitching

Definition at line 230 of file SimParameters.h.

Bool SimParameters::vdwGeometricSigma

Definition at line 927 of file SimParameters.h.

BigReal SimParameters::vdwscale14

Definition at line 921 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::velDcdFilename[128]

Definition at line 202 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::velDcdFrequency

Definition at line 194 of file SimParameters.h.

Bool SimParameters::verboseTopology

Definition at line 154 of file SimParameters.h.

int SimParameters::watmodel

Definition at line 109 of file SimParameters.h.

Bool SimParameters::wrapAll

Definition at line 183 of file SimParameters.h.

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

Bool SimParameters::wrapNearest

Definition at line 184 of file SimParameters.h.

Referenced by ParallelIOMgr::recvFinalClusterCoor().

Bool SimParameters::wrapWater

Definition at line 182 of file SimParameters.h.

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

char SimParameters::xstFilename[128]

Definition at line 204 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

int SimParameters::xstFrequency

Definition at line 198 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::zeroMomentum

Definition at line 180 of file SimParameters.h.

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

Bool SimParameters::zeroMomentumAlt

Definition at line 181 of file SimParameters.h.

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


The documentation for this class was generated from the following files:
Generated on Mon Sep 25 01:17:20 2017 for NAMD by  doxygen 1.4.7