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 ()
static void pme_select ()

Public Attributes

Bool lonepairs
int watmodel
Bool LJcorrection
BigReal dt
int N
int stepsPerCycle
zVector cellBasisVector1
zVector cellBasisVector2
zVector cellBasisVector3
zVector cellOrigin
Lattice lattice
int nonbondedFrequency
int fullElectFrequency
BigReal fmaTheta
int ldBalancer
int ldbStrategy
int ldbPeriod
int firstLdbStep
int lastLdbStep
int hybridGroupSize
BigReal ldbBackgroundScaling
BigReal ldbPMEBackgroundScaling
BigReal ldbHomeBackgroundScaling
BigReal ldbRelativeGrainsize
int traceStartStep
int numTraceSteps
Bool outputMaps
Bool simulateInitialMapping
int simulatedPEs
int simulatedNodeSize
Bool disableTopology
Bool verboseTopology
Bool benchTimestep
int useCkLoop
int twoAwayX
int twoAwayY
int twoAwayZ
int maxPatches
Bool ldbUnloadPME
Bool ldbUnloadZero
Bool ldbUnloadOne
Bool ldbUnloadOutputPEs
Bool noPatchesOnZero
Bool noPatchesOnOutputPEs
Bool noPatchesOnOne
BigReal initialTemp
Bool comMove
Bool zeroMomentum
Bool zeroMomentumAlt
Bool wrapWater
Bool wrapAll
Bool wrapNearest
BigReal dielectric
ExclusionSettings exclude
BigReal scale14
BigReal nonbondedScaling
int dcdFrequency
int dcdUnitCell
int velDcdFrequency
int forceDcdFrequency
int xstFrequency
char auxFilename [128]
char dcdFilename [128]
char velDcdFilename [128]
char forceDcdFilename [128]
char xstFilename [128]
char outputFilename [128]
char restartFilename [128]
int restartFrequency
Bool restartSave
Bool restartSaveDcd
Bool binaryRestart
Bool binaryOutput
BigReal cutoff
BigReal margin
BigReal patchDimension
BigReal limitDist
Bool switchingActive
Bool vdwForceSwitching
BigReal switchingDist
Bool martiniSwitching
Bool martiniDielAllow
BigReal pairlistDist
int pairlistMinProcs
int usePairlists
int pairlistsPerCycle
BigReal pairlistShrink
BigReal pairlistGrow
BigReal pairlistTrigger
int outputPairlists
Bool constraintsOn
int constraintExp
Bool gridforceOn
Bool gridforceVolts
zVector gridforceScale
Bool gridforceContA1
Bool gridforceContA2
Bool gridforceContA3
zVector gridforceVOffset
Bool gridforceLite
Bool gridforcechecksize
Bool mgridforceOn
MGridforceParamsList mgridforcelist
Bool selectConstraintsOn
Bool constrXOn
Bool constrYOn
Bool constrZOn
Bool sphericalConstraintsOn
zVector sphericalConstrCenter
BigReal constraintScaling
Bool paraTypeXplorOn
Bool paraTypeCharmmOn
Bool goGroPair
Bool goForcesOn
char goParameters [128]
char goCoordinates [128]
GoChoices goMethod
Bool movingConstraintsOn
zVector movingConsVel
Bool rotConstraintsOn
zVector rotConsAxis
zVector rotConsPivot
BigReal rotConsVel
Bool movDragOn
char movDragFile [128]
BigReal movDragGlobVel
char movDragVelFile [128]
Bool rotDragOn
char rotDragFile [128]
char rotDragAxisFile [128]
char rotDragPivotFile [128]
BigReal rotDragGlobVel
char rotDragVelFile [128]
Bool consTorqueOn
char consTorqueFile [128]
char consTorqueAxisFile [128]
char consTorquePivotFile [128]
BigReal consTorqueGlobVal
char consTorqueValFile [128]
Bool SMDOn
BigReal SMDVel
zVector SMDDir
BigReal SMDk
BigReal SMDk2
char SMDFile [128]
int SMDOutputFreq
Bool tabulatedEnergies
int tableNumTypes
char tabulatedEnergiesFile [128]
char tableInterpType [128]
Real tableSpacing
BigReal tableMaxDist
Bool TMDOn
Bool TMDDiffRMSD
BigReal TMDk
char TMDFile [128]
char TMDFile2 [128]
int TMDOutputFreq
int TMDFirstStep
int TMDLastStep
BigReal TMDInitialRMSD
BigReal TMDFinalRMSD
Bool symmetryOn
Bool symmetryScaleForces
BigReal symmetryk
char symmetrykfile [128]
char symmetryFile [128]
char symmetryMatrixFile [128]
int symmetryFirstStep
int symmetryLastStep
int symmetryFirstFullStep
int symmetryLastFullStep
Bool alchOnAtStartup
Bool alchFepOnAtStartup
Bool alchThermIntOnAtStartup
Bool alchOn
Bool alchFepOn
Bool alchThermIntOn
Bool alchFepWCARepuOn
Bool alchFepWCADispOn
Bool alchFepElecOn
Bool alchFepWhamOn
int alchMethod
BigReal alchLambda
BigReal alchLambda2
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 983 of file SimParameters.h.

00983 : mgridforcelist(), parseopts(0) {};

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

Definition at line 984 of file SimParameters.h.

References initialize_config_data().

00984                                                  : mgridforcelist(), parseopts(0) {
00985           initialize_config_data(c,cwd);
00986         };

SimParameters::~SimParameters (  )  [inline]

Definition at line 987 of file SimParameters.h.

00987 {};


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 7010 of file SimParameters.C.

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

07010                                                          {
07011   // Convenience function for staggered lambda scaling
07012   return (lambda >= alchBondLambdaEnd ? 1. : lambda / alchBondLambdaEnd);
07013 }

BigReal SimParameters::getCurrentLambda ( const   int  ) 

Definition at line 6957 of file SimParameters.C.

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

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

06957                                                       {
06958   /*Get lambda at the current step. 
06959 
06960    If alchLambdaFreq = 0, return alchLambda. For positive values of 
06961    alchLambdaFreq, apply a linear stepwise schedule from alchLambda to 
06962    alchLambda2:
06963 
06964    l(t) = l + (l2 - l)*[dn / (N - n0)]*{floor[(n - n0)/dn] + 1}
06965 
06966    n - the current time step
06967    n0 - step at which switching begins (default = 0)
06968    N - total steps in the simulation
06969    dn - alchLambdaFreq (increment frequency, in steps)
06970    l/l2 - alchLambda/alchLambda2
06971  
06972    Note that each step _begins_ by incrementing alchLambda and then integrates
06973    in time. This means that the first and last switch steps may not behave as
06974    immediately expected - at step 0, alchLambda is NOT evaluated and at step N
06975    no step occurs because alchLambda2 has already been reached.
06976   */
06977   if ( alchLambdaFreq > 0 && step >= alchEquilSteps ) {
06978     if ( step == N ) {
06979       return alchLambda2;
06980     }
06981     else {
06982       const int timeOrigin = firstTimestep + alchEquilSteps;
06983       const BigReal alchLambdaDelta = getLambdaDelta();
06984       const BigReal increment = (step - timeOrigin) / BigReal(alchLambdaFreq);
06985       return alchLambda + alchLambdaDelta*(floor(increment) + 1);
06986     }
06987   }
06988   else {
06989     return alchLambda;
06990   }
06991 }

BigReal SimParameters::getElecLambda ( const   BigReal  ) 

Definition at line 6999 of file SimParameters.C.

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

06999                                                          {
07000   // Convenience function for staggered lambda scaling
07001   return (lambda <= alchElecLambdaStart ? 0.
07002           : (lambda - alchElecLambdaStart) / (1. - alchElecLambdaStart));
07003 }

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

Definition at line 97 of file SimParameters.C.

References ParseOptions::getfromptr().

00097                                                                     {
00098   if ( parseopts ) return parseopts->getfromptr(name,outbuf);
00099   else return 0;
00100 }

BigReal SimParameters::getLambdaDelta ( void   ) 

Definition at line 6993 of file SimParameters.C.

References alchEquilSteps, alchLambdaFreq, and firstTimestep.

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

06993                                           {
06994   // Increment by which Lambda changes.
06995   return ((alchLambda2 - alchLambda)*alchLambdaFreq
06996           / BigReal(N - firstTimestep - alchEquilSteps));
06997 }

BigReal SimParameters::getVdwLambda ( const   BigReal  ) 

Definition at line 7005 of file SimParameters.C.

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

07005                                                         {
07006   // Convenience function for staggered lambda scaling
07007   return (lambda >= alchVdwLambdaEnd ? 1. : lambda / alchVdwLambdaEnd);
07008 }

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

Definition at line 125 of file SimParameters.C.

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

Referenced by SimParameters().

00127 {
00128 
00129    parseopts = new ParseOptions;   //  Object to check consistency of config file
00130    ParseOptions &opts = *parseopts;
00131 
00132    config_parser(opts);
00133 
00135    if (!opts.check_consistency()) 
00136    {
00137       NAMD_die("Internal error in configuration file parser");
00138    }
00139 
00140    // Now, feed the object with the actual configuration options through the
00141    // ParseOptions file and make sure everything is OK
00142    if (!opts.set(*config)) 
00143    {
00144       NAMD_die("ERROR(S) IN THE CONFIGURATION FILE");
00145    }
00146 
00148 
00149    check_config(opts,config,cwd);
00150 
00151    print_config(opts,config,cwd);
00152 
00153 }

int SimParameters::isRecvSpanningTreeOn (  )  [inline]

Definition at line 1009 of file SimParameters.h.

References proxyRecvSpanningTree.

Referenced by Node::startup().

01009 { return proxyRecvSpanningTree == 1; }

int SimParameters::isRecvSpanningTreeUnset (  )  [inline]

Definition at line 1010 of file SimParameters.h.

References proxyRecvSpanningTree.

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

01010 { return proxyRecvSpanningTree == -1; }

int SimParameters::isSendSpanningTreeOn (  )  [inline]

Definition at line 1007 of file SimParameters.h.

References proxySendSpanningTree.

Referenced by Node::startup().

01007 { return proxySendSpanningTree == 1; }

int SimParameters::isSendSpanningTreeUnset (  )  [inline]

Definition at line 1008 of file SimParameters.h.

References proxySendSpanningTree.

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

01008 { return proxySendSpanningTree == -1; }

int SimParameters::issetinparseopts ( const char *  name  ) 

Definition at line 107 of file SimParameters.C.

References ParseOptions::issetfromptr().

00107                                                     {
00108   if ( parseopts ) return parseopts->issetfromptr(name);
00109   else return -1;
00110 }

int SimParameters::istrueinparseopts ( const char *  name  ) 

Definition at line 102 of file SimParameters.C.

References ParseOptions::istruefromptr().

00102                                                      {
00103   if ( parseopts ) return parseopts->istruefromptr(name);
00104   else return -1;
00105 }

void SimParameters::nonbonded_select (  )  [static]

Definition at line 383 of file SimParameters.C.

References ComputeNonbondedUtil::select().

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

00383                                      {
00384     ComputeNonbondedUtil::select();
00385 }

void SimParameters::pme_select (  )  [static]

Definition at line 387 of file SimParameters.C.

References ComputePmeUtil::select().

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

00387                                {
00388   ComputePmeUtil::select();
00389 }

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

Definition at line 2254 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.

02254                                                                             {
02255 
02256      if ( ! latptr ) {
02257        iout << iINFO << "EXTENDED SYSTEM FILE   " << filename << "\n" << endi;
02258      }
02259 
02260      ifstream xscFile(filename);
02261      if ( ! xscFile ) NAMD_die("Unable to open extended system file.\n");
02262 
02263      char labels[1024];
02264      do {
02265        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02266        xscFile.getline(labels,1023);
02267      } while ( strncmp(labels,"#$LABELS ",9) );
02268 
02269      int a_x, a_y, a_z, b_x, b_y, b_z, c_x, c_y, c_z;
02270      a_x = a_y = a_z = b_x = b_y = b_z = c_x = c_y = c_z = -1;
02271      int o_x, o_y, o_z, s_u, s_v, s_w, s_x, s_y, s_z;
02272      o_x = o_y = o_z = s_u = s_v = s_w = s_x = s_y = s_z = -1;
02273 
02274      int pos = 0;
02275      char *l_i = labels + 8;
02276      while ( *l_i ) {
02277        if ( *l_i == ' ' ) { ++l_i; continue; }
02278        char *l_i2;
02279        for ( l_i2 = l_i; *l_i2 && *l_i2 != ' '; ++l_i2 );
02280        if ( (l_i2 - l_i) == 3 && (l_i[1] == '_') ) {
02281          if (l_i[0] == 'a' && l_i[2] == 'x') a_x = pos;
02282          if (l_i[0] == 'a' && l_i[2] == 'y') a_y = pos;
02283          if (l_i[0] == 'a' && l_i[2] == 'z') a_z = pos;
02284          if (l_i[0] == 'b' && l_i[2] == 'x') b_x = pos;
02285          if (l_i[0] == 'b' && l_i[2] == 'y') b_y = pos;
02286          if (l_i[0] == 'b' && l_i[2] == 'z') b_z = pos;
02287          if (l_i[0] == 'c' && l_i[2] == 'x') c_x = pos;
02288          if (l_i[0] == 'c' && l_i[2] == 'y') c_y = pos;
02289          if (l_i[0] == 'c' && l_i[2] == 'z') c_z = pos;
02290          if (l_i[0] == 'o' && l_i[2] == 'x') o_x = pos;
02291          if (l_i[0] == 'o' && l_i[2] == 'y') o_y = pos;
02292          if (l_i[0] == 'o' && l_i[2] == 'z') o_z = pos;
02293          if (l_i[0] == 's' && l_i[2] == 'u') s_u = pos;
02294          if (l_i[0] == 's' && l_i[2] == 'v') s_v = pos;
02295          if (l_i[0] == 's' && l_i[2] == 'w') s_w = pos;
02296          if (l_i[0] == 's' && l_i[2] == 'x') s_x = pos;
02297          if (l_i[0] == 's' && l_i[2] == 'y') s_y = pos;
02298          if (l_i[0] == 's' && l_i[2] == 'z') s_z = pos;
02299        }
02300        ++pos;
02301        l_i = l_i2;
02302      }
02303      int numpos = pos;
02304 
02305      for ( pos = 0; pos < numpos; ++pos ) {
02306        double tmp;
02307        xscFile >> tmp;
02308        if ( ! xscFile ) NAMD_die("Error reading extended system file.\n");
02309        if ( pos == a_x ) cellBasisVector1.x = tmp;
02310        if ( pos == a_y ) cellBasisVector1.y = tmp;
02311        if ( pos == a_z ) cellBasisVector1.z = tmp;
02312        if ( pos == b_x ) cellBasisVector2.x = tmp;
02313        if ( pos == b_y ) cellBasisVector2.y = tmp;
02314        if ( pos == b_z ) cellBasisVector2.z = tmp;
02315        if ( pos == c_x ) cellBasisVector3.x = tmp;
02316        if ( pos == c_y ) cellBasisVector3.y = tmp;
02317        if ( pos == c_z ) cellBasisVector3.z = tmp;
02318        if ( pos == o_x ) cellOrigin.x = tmp;
02319        if ( pos == o_y ) cellOrigin.y = tmp;
02320        if ( pos == o_z ) cellOrigin.z = tmp;
02321        if ( pos == s_u ) strainRate2.x = tmp;
02322        if ( pos == s_v ) strainRate2.y = tmp;
02323        if ( pos == s_w ) strainRate2.z = tmp;
02324        if ( pos == s_x ) strainRate.x = tmp;
02325        if ( pos == s_y ) strainRate.y = tmp;
02326        if ( pos == s_z ) strainRate.z = tmp;
02327      }
02328 
02329    if ( latptr ) {
02330      Lattice test;
02331      test.set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02332     
02333      if ( test.a_p() && ! lattice.a_p() ) {
02334        NAMD_die("cellBasisVector1 added during atom reinitialization");
02335      }
02336      if ( lattice.a_p() && ! test.a_p() ) {
02337        NAMD_die("cellBasisVector1 dropped during atom reinitialization");
02338      }
02339      if ( test.b_p() && ! lattice.b_p() ) {
02340        NAMD_die("cellBasisVector2 added during atom reinitialization");
02341      }
02342      if ( lattice.b_p() && ! test.b_p() ) {
02343        NAMD_die("cellBasisVector2 dropped during atom reinitialization");
02344      }
02345      if ( test.c_p() && ! lattice.c_p() ) {
02346        NAMD_die("cellBasisVector3 added during atom reinitialization");
02347      }
02348      if ( lattice.c_p() && ! test.c_p() ) {
02349        NAMD_die("cellBasisVector3 dropped during atom reinitialization");
02350      }
02351 
02352      latptr->set(cellBasisVector1,cellBasisVector2,cellBasisVector3,cellOrigin);
02353    }
02354 
02355 }

void SimParameters::receive_SimParameters ( MIStream  ) 

Definition at line 6899 of file SimParameters.C.

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

06901 {
06902   msg->get(sizeof(SimParameters),(char*)this);
06903   if ( FFTWWisdomString ) {
06904     int fftwlen;
06905     msg->get(fftwlen);
06906     FFTWWisdomString = new char[fftwlen];
06907     msg->get(fftwlen,FFTWWisdomString);
06908 #ifdef NAMD_FFTW
06909 #ifdef NAMD_FFTW_3
06910     fftwf_import_wisdom_from_string(FFTWWisdomString);
06911 #else
06912     fftw_import_wisdom_from_string(FFTWWisdomString);
06913 #endif
06914 #endif
06915   }
06916   if ( tclBCScript ) {
06917     int tcllen;
06918     msg->get(tcllen);
06919     tclBCScript = new char[tcllen];
06920     msg->get(tcllen,tclBCScript);
06921   }
06922 
06923 #ifdef MEM_OPT_VERSION
06924   int filelen;
06925   msg->get(filelen);
06926   binAtomFile = new char[filelen];
06927   msg->get(filelen, binAtomFile);
06928   
06929   msg->get(filelen);
06930   binCoorFile = new char[filelen];
06931   msg->get(filelen, binCoorFile);
06932 
06933   if(binVelFile) {    
06934     msg->get(filelen);
06935     binVelFile = new char[filelen];
06936     msg->get(filelen, binVelFile);
06937   }
06938 
06939   if(binRefFile) {    
06940     msg->get(filelen);
06941     binRefFile = new char[filelen];
06942     msg->get(filelen, binRefFile);
06943   }
06944 #endif
06945 
06946 
06947   // The simParameters bit copy above put illegal values in the list pointers
06948   // So this resets everything so that unpacking will work.
06949   mgridforcelist.clear();
06950   mgridforcelist.unpack_data(msg);
06951   
06952   delete msg;
06953 }

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

Definition at line 167 of file SimParameters.C.

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

Referenced by Node::scriptParam().

00167                                                                   {
00168 
00169   if ( CkMyRank() ) return;
00170 
00171 #define MAX_SCRIPT_PARAM_SIZE 128
00172 #define SCRIPT_PARSE_BOOL(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atobool(value); return; } }
00173 #define SCRIPT_PARSE_INT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atoi(value); return; } }
00174 #define SCRIPT_PARSE_FLOAT(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value); return; } }
00175 #define SCRIPT_PARSE_MOD_FLOAT(NAME,VAR,MOD) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR) = atof(value) MOD; return; } }
00176 #define SCRIPT_PARSE_VECTOR(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { (VAR).set(value); return; } }
00177 #define SCRIPT_PARSE_STRING(NAME,VAR) { if ( ! strncasecmp(param,(NAME),MAX_SCRIPT_PARAM_SIZE) ) { strcpy(VAR,value); return; } }
00178 
00179   SCRIPT_PARSE_FLOAT("scriptArg1",scriptArg1)
00180   SCRIPT_PARSE_FLOAT("scriptArg2",scriptArg2)
00181   SCRIPT_PARSE_FLOAT("scriptArg3",scriptArg3)
00182   SCRIPT_PARSE_FLOAT("scriptArg4",scriptArg4)
00183   SCRIPT_PARSE_FLOAT("scriptArg5",scriptArg5)
00184   SCRIPT_PARSE_INT("scriptIntArg1",scriptIntArg1)
00185   SCRIPT_PARSE_INT("scriptIntArg2",scriptIntArg2)
00186   SCRIPT_PARSE_STRING("scriptStringArg1",scriptStringArg1)
00187   SCRIPT_PARSE_STRING("scriptStringArg2",scriptStringArg2)
00188   SCRIPT_PARSE_INT("numsteps",N)
00189   if ( ! strncasecmp(param,"firsttimestep",MAX_SCRIPT_PARAM_SIZE) ) {
00190     N = firstTimestep = atoi(value); return;
00191   }
00192   SCRIPT_PARSE_FLOAT("reassignTemp",reassignTemp)
00193   SCRIPT_PARSE_FLOAT("rescaleTemp",rescaleTemp)
00194   SCRIPT_PARSE_BOOL("velocityQuenching",minimizeOn)
00195   SCRIPT_PARSE_BOOL("maximumMove",maximumMove)
00196   // SCRIPT_PARSE_BOOL("Langevin",langevinOn)
00197   if ( ! strncasecmp(param,"Langevin",MAX_SCRIPT_PARAM_SIZE) ) {
00198     langevinOn = atobool(value);
00199     if ( langevinOn && ! langevinOnAtStartup ) {
00200       NAMD_die("Langevin must be enabled at startup to disable and re-enable in script.");
00201     }
00202     return;
00203   }
00204   SCRIPT_PARSE_FLOAT("langevinTemp",langevinTemp)
00205   SCRIPT_PARSE_BOOL("langevinBAOAB",langevin_useBAOAB) // [!!] Use the BAOAB integrator or not
00206   SCRIPT_PARSE_FLOAT("loweAndersenTemp",loweAndersenTemp) // BEGIN LA, END LA
00207   SCRIPT_PARSE_FLOAT("initialTemp",initialTemp)
00208   SCRIPT_PARSE_BOOL("useGroupPressure",useGroupPressure)
00209   SCRIPT_PARSE_BOOL("useFlexibleCell",useFlexibleCell)
00210   SCRIPT_PARSE_BOOL("useConstantArea",useConstantArea)
00211   SCRIPT_PARSE_BOOL("fixCellDims",fixCellDims)
00212   SCRIPT_PARSE_BOOL("fixCellDimX",fixCellDimX)
00213   SCRIPT_PARSE_BOOL("fixCellDimY",fixCellDimY)
00214   SCRIPT_PARSE_BOOL("fixCellDimZ",fixCellDimZ)
00215   SCRIPT_PARSE_BOOL("useConstantRatio",useConstantRatio)
00216   SCRIPT_PARSE_BOOL("LangevinPiston",langevinPistonOn)
00217   SCRIPT_PARSE_MOD_FLOAT("LangevinPistonTarget",
00218                         langevinPistonTarget,/PRESSUREFACTOR)
00219   SCRIPT_PARSE_FLOAT("LangevinPistonPeriod",langevinPistonPeriod)
00220   SCRIPT_PARSE_FLOAT("LangevinPistonDecay",langevinPistonDecay)
00221   SCRIPT_PARSE_FLOAT("LangevinPistonTemp",langevinPistonTemp)
00222   SCRIPT_PARSE_MOD_FLOAT("SurfaceTensionTarget",
00223                         surfaceTensionTarget,*(100.0/PRESSUREFACTOR))
00224   SCRIPT_PARSE_BOOL("BerendsenPressure",berendsenPressureOn)
00225   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureTarget",
00226                         berendsenPressureTarget,/PRESSUREFACTOR)
00227   SCRIPT_PARSE_MOD_FLOAT("BerendsenPressureCompressibility",
00228                         berendsenPressureCompressibility,*PRESSUREFACTOR)
00229   SCRIPT_PARSE_FLOAT("BerendsenPressureRelaxationTime",
00230                                 berendsenPressureRelaxationTime)
00231   SCRIPT_PARSE_FLOAT("constraintScaling",constraintScaling)
00232   SCRIPT_PARSE_FLOAT("consForceScaling",consForceScaling)
00233   SCRIPT_PARSE_BOOL("drudeHardWall",drudeHardWallOn)
00234   SCRIPT_PARSE_FLOAT("drudeBondConst",drudeBondConst)
00235   SCRIPT_PARSE_FLOAT("drudeBondLen",drudeBondLen)
00236   SCRIPT_PARSE_STRING("outputname",outputFilename)
00237   SCRIPT_PARSE_INT("outputEnergies",outputEnergies)
00238   SCRIPT_PARSE_STRING("restartname",restartFilename)
00239   SCRIPT_PARSE_INT("DCDfreq",dcdFrequency)
00240   if ( ! strncasecmp(param,"DCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
00241     close_dcdfile();  // *** implemented in Output.C ***
00242     strcpy(dcdFilename,value);
00243     return;
00244   }
00245   if ( ! strncasecmp(param,"velDCDfile",MAX_SCRIPT_PARAM_SIZE) ) { 
00246     close_veldcdfile();  // *** implemented in Output.C ***
00247     strcpy(velDcdFilename,value);
00248     return;
00249   }
00250   SCRIPT_PARSE_STRING("tclBCArgs",tclBCArgs)
00251   SCRIPT_PARSE_VECTOR("eField",eField)
00252   SCRIPT_PARSE_FLOAT("eFieldFreq",eFieldFreq)
00253   SCRIPT_PARSE_FLOAT("eFieldPhase",eFieldPhase) 
00254   SCRIPT_PARSE_FLOAT("accelMDE",accelMDE) 
00255   SCRIPT_PARSE_FLOAT("accelMDalpha",accelMDalpha) 
00256   SCRIPT_PARSE_FLOAT("accelMDTE",accelMDTE) 
00257   SCRIPT_PARSE_FLOAT("accelMDTalpha",accelMDTalpha) 
00258   SCRIPT_PARSE_FLOAT("accelMDGSigma0P",accelMDGSigma0P) 
00259   SCRIPT_PARSE_FLOAT("accelMDGSigma0D",accelMDGSigma0D) 
00260   SCRIPT_PARSE_STRING("accelMDGRestartFile",accelMDGRestartFile)
00261   SCRIPT_PARSE_VECTOR("stirAxis",stirAxis)
00262   SCRIPT_PARSE_VECTOR("stirPivot",stirPivot)
00263   if ( ! strncasecmp(param,"mgridforcescale",MAX_SCRIPT_PARAM_SIZE) ) {
00264     NAMD_die("Can't yet modify mgridforcescale in a script");
00265     return;
00266   }
00267   if ( ! strncasecmp(param,"mgridforcevoff",MAX_SCRIPT_PARAM_SIZE) ) {
00268     NAMD_die("Can't yet modify mgridforcevoff in a script");
00269     return;
00270   }
00271    
00272   if ( ! strncasecmp(param,"fixedatoms",MAX_SCRIPT_PARAM_SIZE) ) {
00273     if ( ! fixedAtomsOn )
00274       NAMD_die("FixedAtoms may not be enabled in a script.");
00275     if ( ! fixedAtomsForces )
00276       NAMD_die("To use fixedAtoms in script first use fixedAtomsForces yes.");
00277     fixedAtomsOn = atobool(value);
00278     return;
00279   }
00280 
00281 //fepb
00282   if ( ! strncasecmp(param,"alch",MAX_SCRIPT_PARAM_SIZE) ) {
00283     alchOn = atobool(value);
00284     if ( alchOn && ! alchOnAtStartup ) {
00285        NAMD_die("Alchemy must be enabled at startup to disable and re-enable in script.");
00286     }
00287     alchFepOn = alchOn && alchFepOnAtStartup;
00288     alchThermIntOn = alchOn && alchThermIntOnAtStartup;
00289     ComputeNonbondedUtil::select();
00290     if ( PMEOn ) ComputePmeUtil::select();
00291     return;
00292   }
00293   SCRIPT_PARSE_INT("alchEquilSteps",alchEquilSteps)
00294 
00295   if ( ! strncasecmp(param,"alchRepLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00296     alchRepLambda = atof(value);
00297     alchFepWCARepuOn = true;
00298     alchFepWCADispOn = false;
00299     alchFepElecOn    = false;
00300     ComputeNonbondedUtil::select();
00301     return;
00302   }
00303 
00304   if ( ! strncasecmp(param,"alchDispLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00305     alchDispLambda = atof(value);
00306     alchFepWCARepuOn = false;
00307     alchFepWCADispOn = true;
00308     alchFepElecOn    = false;
00309     ComputeNonbondedUtil::select();
00310     return;
00311   }
00312 
00313   if ( ! strncasecmp(param,"alchElecLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00314     alchElecLambda = atof(value);
00315     alchFepWCARepuOn = false;
00316     alchFepWCADispOn = false;
00317     alchFepElecOn    = true;
00318     ComputeNonbondedUtil::select();
00319     return;
00320   }
00321 
00322 
00323   if ( ! strncasecmp(param,"alchFepWCArcut1",MAX_SCRIPT_PARAM_SIZE) ) {
00324     alchFepWCArcut1 = atof(value);
00325     ComputeNonbondedUtil::select();
00326     return;
00327   }
00328 
00329   if ( ! strncasecmp(param,"alchFepWCArcut2",MAX_SCRIPT_PARAM_SIZE) ) {
00330     alchFepWCArcut2 = atof(value);
00331     ComputeNonbondedUtil::select();
00332     return;
00333   }
00334 
00335   if ( ! strncasecmp(param,"alchFepWCArcut3",MAX_SCRIPT_PARAM_SIZE) ) {
00336     alchFepWCArcut3 = atof(value);
00337     ComputeNonbondedUtil::select();
00338     return;
00339   }
00340 
00341   if ( ! strncasecmp(param,"alchLambda",MAX_SCRIPT_PARAM_SIZE) ) {
00342     alchLambda = atof(value);
00343     if ( alchLambda < 0.0 || 1.0 < alchLambda ) {
00344       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00345     }
00346     ComputeNonbondedUtil::select();
00347     return;
00348   }
00349 
00350   if ( ! strncasecmp(param,"alchLambda2",MAX_SCRIPT_PARAM_SIZE) ) {
00351     alchLambda2 = atof(value);
00352     if ( alchLambda2 < 0.0 || 1.0 < alchLambda2 ) {
00353       NAMD_die("Alchemical lambda values should be in the range [0.0, 1.0]\n");
00354     }
00355     ComputeNonbondedUtil::select();
00356     return;
00357   }
00358 
00359   if ( ! strncasecmp(param,"alchLambdaFreq",MAX_SCRIPT_PARAM_SIZE) ) {
00360     alchLambdaFreq = atoi(value);
00361     ComputeNonbondedUtil::select();
00362     return;
00363   }
00364 //fepe
00365 
00366   if ( ! strncasecmp(param,"nonbondedScaling",MAX_SCRIPT_PARAM_SIZE) ) {
00367     nonbondedScaling = atof(value);
00368     ComputeNonbondedUtil::select();
00369     return;
00370   }
00371   if ( ! strncasecmp(param,"commOnly",MAX_SCRIPT_PARAM_SIZE) ) {
00372     commOnly = atobool(value);
00373     ComputeNonbondedUtil::select();
00374     return;
00375   }
00376 
00377   char *error = new char[2 * MAX_SCRIPT_PARAM_SIZE + 100];
00378   sprintf(error,"Setting parameter %s from script failed!\n",param);
00379   NAMD_die(error);
00380 
00381 }

void SimParameters::send_SimParameters ( MOStream  ) 

Definition at line 6841 of file SimParameters.C.

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

06843 {
06844   /*MOStream *msg = com_obj->newOutputStream(ALLBUTME, SIMPARAMSTAG, BUFSIZE);
06845   if ( msg == NULL )
06846   {
06847     NAMD_die("memory allocation failed in SimParameters::send_SimParameters");
06848   }*/
06849 
06850   msg->put(sizeof(SimParameters),(char*)this);
06851   if ( FFTWWisdomString ) {
06852     int fftwlen = strlen(FFTWWisdomString) + 1;
06853     msg->put(fftwlen);
06854     msg->put(fftwlen,FFTWWisdomString);
06855   }
06856   if ( tclBCScript ) {
06857     int tcllen = strlen(tclBCScript) + 1;
06858     msg->put(tcllen);
06859     msg->put(tcllen,tclBCScript);
06860   }
06861 
06862 #ifdef MEM_OPT_VERSION
06863   int filelen = strlen(binAtomFile)+1;
06864   msg->put(filelen);
06865   msg->put(filelen, binAtomFile);
06866 
06867   filelen = strlen(binCoorFile)+1;
06868   msg->put(filelen);
06869   msg->put(filelen, binCoorFile);
06870 
06871   if(binVelFile) {
06872     filelen = strlen(binVelFile)+1;
06873     msg->put(filelen);
06874     msg->put(filelen, binVelFile);
06875   }
06876 
06877   if(binRefFile) {
06878     filelen = strlen(binRefFile)+1;
06879     msg->put(filelen);
06880     msg->put(filelen, binRefFile);
06881   }
06882 #endif
06883 
06884   mgridforcelist.pack_data(msg);
06885   
06886   msg->end();
06887 }


Member Data Documentation

int SimParameters::aaAngleExp

Definition at line 900 of file SimParameters.h.

BigReal SimParameters::accelMDalpha

Definition at line 576 of file SimParameters.h.

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

Bool SimParameters::accelMDDebugOn

Definition at line 571 of file SimParameters.h.

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

Bool SimParameters::accelMDdihe

Definition at line 569 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 570 of file SimParameters.h.

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

BigReal SimParameters::accelMDE

Definition at line 575 of file SimParameters.h.

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

BigReal SimParameters::accelMDFirstStep

Definition at line 572 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDG

Definition at line 580 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDPrepSteps

Definition at line 584 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGcMDSteps

Definition at line 582 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiPrepSteps

Definition at line 585 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGEquiSteps

Definition at line 583 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

int SimParameters::accelMDGiE

Definition at line 581 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGresetVaftercmd

Definition at line 590 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

Bool SimParameters::accelMDGRestart

Definition at line 588 of file SimParameters.h.

Referenced by Controller::rescaleaccelMD().

char SimParameters::accelMDGRestartFile[128]

Definition at line 589 of file SimParameters.h.

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

BigReal SimParameters::accelMDGSigma0D

Definition at line 587 of file SimParameters.h.

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

BigReal SimParameters::accelMDGSigma0P

Definition at line 586 of file SimParameters.h.

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

BigReal SimParameters::accelMDLastStep

Definition at line 573 of file SimParameters.h.

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

Bool SimParameters::accelMDOn

Definition at line 568 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 574 of file SimParameters.h.

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

BigReal SimParameters::accelMDTalpha

Definition at line 578 of file SimParameters.h.

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

BigReal SimParameters::accelMDTE

Definition at line 577 of file SimParameters.h.

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

BigReal SimParameters::adaptTempAutoDt

Definition at line 601 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempBins

Definition at line 602 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempCgamma

Definition at line 604 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempDebug

Definition at line 594 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

BigReal SimParameters::adaptTempDt

Definition at line 603 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

int SimParameters::adaptTempFirstStep

Definition at line 595 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

int SimParameters::adaptTempFreq

Definition at line 598 of file SimParameters.h.

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

char SimParameters::adaptTempInFile[128]

Definition at line 607 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::adaptTempLangevin

Definition at line 605 of file SimParameters.h.

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

int SimParameters::adaptTempLastStep

Definition at line 596 of file SimParameters.h.

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

Bool SimParameters::adaptTempOn

Definition at line 593 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 597 of file SimParameters.h.

Referenced by Controller::adaptTempUpdate().

Bool SimParameters::adaptTempRandom

Definition at line 610 of file SimParameters.h.

Bool SimParameters::adaptTempRescale

Definition at line 606 of file SimParameters.h.

Referenced by Controller::rescaleVelocities().

char SimParameters::adaptTempRestartFile[128]

Definition at line 608 of file SimParameters.h.

int SimParameters::adaptTempRestartFreq

Definition at line 609 of file SimParameters.h.

Referenced by Controller::adaptTempWriteRestart().

BigReal SimParameters::adaptTempTmax

Definition at line 600 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

BigReal SimParameters::adaptTempTmin

Definition at line 599 of file SimParameters.h.

Referenced by Controller::adaptTempInit().

Bool SimParameters::alchBondDecouple

Definition at line 422 of file SimParameters.h.

BigReal SimParameters::alchBondLambdaEnd

Definition at line 416 of file SimParameters.h.

Bool SimParameters::alchDecouple

Definition at line 421 of file SimParameters.h.

BigReal SimParameters::alchDispLambda

Definition at line 393 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambda

Definition at line 394 of file SimParameters.h.

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

BigReal SimParameters::alchElecLambdaStart

Definition at line 405 of file SimParameters.h.

Bool SimParameters::alchEnsembleAvg

Definition at line 400 of file SimParameters.h.

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

int SimParameters::alchEquilSteps

Definition at line 402 of file SimParameters.h.

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

Bool SimParameters::alchFepElecOn

Definition at line 383 of file SimParameters.h.

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

Bool SimParameters::alchFepOn

Definition at line 379 of file SimParameters.h.

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

Bool SimParameters::alchFepOnAtStartup

Definition at line 376 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::alchFepWCADispOn

Definition at line 382 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut1

Definition at line 395 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut2

Definition at line 396 of file SimParameters.h.

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

BigReal SimParameters::alchFepWCArcut3

Definition at line 397 of file SimParameters.h.

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

Bool SimParameters::alchFepWCARepuOn

Definition at line 381 of file SimParameters.h.

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

Bool SimParameters::alchFepWhamOn

Definition at line 384 of file SimParameters.h.

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

BigReal SimParameters::alchLambda

Definition at line 386 of file SimParameters.h.

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

BigReal SimParameters::alchLambda2

Definition at line 387 of file SimParameters.h.

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

int SimParameters::alchLambdaFreq

Definition at line 388 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 385 of file SimParameters.h.

Bool SimParameters::alchOn

Definition at line 378 of file SimParameters.h.

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

Bool SimParameters::alchOnAtStartup

Definition at line 375 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::alchOutFile[128]

Definition at line 401 of file SimParameters.h.

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

int SimParameters::alchOutFreq

Definition at line 399 of file SimParameters.h.

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

BigReal SimParameters::alchRepLambda

Definition at line 392 of file SimParameters.h.

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

BigReal SimParameters::alchTemp

Definition at line 398 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOn

Definition at line 380 of file SimParameters.h.

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

Bool SimParameters::alchThermIntOnAtStartup

Definition at line 377 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::alchVdwLambdaEnd

Definition at line 411 of file SimParameters.h.

Referenced by Controller::printEnergies().

BigReal SimParameters::alchVdwShiftCoeff

Definition at line 403 of file SimParameters.h.

BigReal SimParameters::alpha_cutoff

Definition at line 502 of file SimParameters.h.

BigReal SimParameters::alpha_max

Definition at line 503 of file SimParameters.h.

Bool SimParameters::amberOn

Definition at line 921 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 634 of file SimParameters.h.

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

int SimParameters::berendsenPressureFreq

Definition at line 636 of file SimParameters.h.

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

Bool SimParameters::berendsenPressureOn

Definition at line 632 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureRelaxationTime

Definition at line 635 of file SimParameters.h.

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

BigReal SimParameters::berendsenPressureTarget

Definition at line 633 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 959 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binCoorFile

Definition at line 960 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binRefFile

Definition at line 962 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

char* SimParameters::binVelFile

Definition at line 961 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

int SimParameters::bondedCUDA

Definition at line 745 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 556 of file SimParameters.h.

BigReal SimParameters::COLDRate

Definition at line 558 of file SimParameters.h.

BigReal SimParameters::COLDTemp

Definition at line 559 of file SimParameters.h.

Bool SimParameters::colvarsOn

Definition at line 533 of file SimParameters.h.

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

Bool SimParameters::commOnly

Definition at line 860 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 968 of file SimParameters.h.

char SimParameters::consForceFile[128]

Definition at line 812 of file SimParameters.h.

Bool SimParameters::consForceOn

Definition at line 811 of file SimParameters.h.

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

BigReal SimParameters::consForceScaling

Definition at line 813 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 522 of file SimParameters.h.

BigReal SimParameters::coulomb_radius_offset

Definition at line 496 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 784 of file SimParameters.h.

int SimParameters::cylindricalBCexp1

Definition at line 789 of file SimParameters.h.

int SimParameters::cylindricalBCexp2

Definition at line 790 of file SimParameters.h.

BigReal SimParameters::cylindricalBCk1

Definition at line 791 of file SimParameters.h.

BigReal SimParameters::cylindricalBCk2

Definition at line 792 of file SimParameters.h.

BigReal SimParameters::cylindricalBCl1

Definition at line 787 of file SimParameters.h.

BigReal SimParameters::cylindricalBCl2

Definition at line 788 of file SimParameters.h.

Bool SimParameters::cylindricalBCOn

Definition at line 781 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::cylindricalBCr1

Definition at line 785 of file SimParameters.h.

BigReal SimParameters::cylindricalBCr2

Definition at line 786 of file SimParameters.h.

zVector SimParameters::cylindricalCenter

Definition at line 783 of file SimParameters.h.

BigReal SimParameters::daCutoffDist

Definition at line 907 of file SimParameters.h.

BigReal SimParameters::daOffDist

Definition at line 907 of file SimParameters.h.

BigReal SimParameters::daOnDist

Definition at line 907 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 903 of file SimParameters.h.

BigReal SimParameters::dhaOffAngle

Definition at line 903 of file SimParameters.h.

BigReal SimParameters::dhaOnAngle

Definition at line 903 of file SimParameters.h.

BigReal SimParameters::dielectric

Definition at line 185 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::dihedralOn

Definition at line 555 of file SimParameters.h.

Bool SimParameters::disableTopology

Definition at line 153 of file SimParameters.h.

int SimParameters::distAttExp

Definition at line 900 of file SimParameters.h.

int SimParameters::distRepExp

Definition at line 900 of file SimParameters.h.

BigReal SimParameters::drudeBondConst

Definition at line 514 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::drudeBondLen

Definition at line 512 of file SimParameters.h.

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

BigReal SimParameters::drudeDamping

Definition at line 510 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::drudeHardWallOn

Definition at line 508 of file SimParameters.h.

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

BigReal SimParameters::drudeNbtholeCut

Definition at line 515 of file SimParameters.h.

Bool SimParameters::drudeOn

Definition at line 507 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 509 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 796 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::eFieldFreq

Definition at line 797 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::eFieldNormalized

Definition at line 795 of file SimParameters.h.

Bool SimParameters::eFieldOn

Definition at line 794 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::eFieldPhase

Definition at line 798 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 621 of file SimParameters.h.

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

char SimParameters::extCoordFilename[128]

Definition at line 433 of file SimParameters.h.

char SimParameters::extForceFilename[128]

Definition at line 434 of file SimParameters.h.

char SimParameters::extForcesCommand[256]

Definition at line 432 of file SimParameters.h.

Bool SimParameters::extForcesOn

Definition at line 431 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::extraBondsOn

Definition at line 809 of file SimParameters.h.

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

Bool SimParameters::FFTWEstimate

Definition at line 750 of file SimParameters.h.

Bool SimParameters::FFTWPatient

Definition at line 751 of file SimParameters.h.

Bool SimParameters::FFTWUseWisdom

Definition at line 752 of file SimParameters.h.

char SimParameters::FFTWWisdomFile[128]

Definition at line 753 of file SimParameters.h.

char* SimParameters::FFTWWisdomString

Definition at line 754 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 832 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 627 of file SimParameters.h.

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

Bool SimParameters::fixCellDimX

Definition at line 628 of file SimParameters.h.

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

Bool SimParameters::fixCellDimY

Definition at line 629 of file SimParameters.h.

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

Bool SimParameters::fixCellDimZ

Definition at line 630 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsForceOutput

Definition at line 537 of file SimParameters.h.

Bool SimParameters::fixedAtomsForces

Definition at line 536 of file SimParameters.h.

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

Bool SimParameters::fixedAtomsOn

Definition at line 535 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 674 of file SimParameters.h.

Bool SimParameters::FMAFFTOn

Definition at line 673 of file SimParameters.h.

int SimParameters::FMALevels

Definition at line 671 of file SimParameters.h.

int SimParameters::FMAMp

Definition at line 672 of file SimParameters.h.

Bool SimParameters::FMAOn

Definition at line 670 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 718 of file SimParameters.h.

Bool SimParameters::FMMOn

Definition at line 717 of file SimParameters.h.

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

BigReal SimParameters::FMMPadding

Definition at line 719 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 531 of file SimParameters.h.

Referenced by ParallelIOMgr::freeMolSpace().

BigReal SimParameters::fsMax

Definition at line 493 of file SimParameters.h.

Bool SimParameters::fullDirectOn

Definition at line 676 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 500 of file SimParameters.h.

BigReal SimParameters::gbis_delta

Definition at line 499 of file SimParameters.h.

BigReal SimParameters::gbis_gamma

Definition at line 501 of file SimParameters.h.

Bool SimParameters::GBISOn

Definition at line 492 of file SimParameters.h.

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

Bool SimParameters::GBISserOn

Definition at line 494 of file SimParameters.h.

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

Bool SimParameters::genCompressedPsf

Definition at line 943 of file SimParameters.h.

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

Bool SimParameters::globalForcesOn

Definition at line 523 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::globalOn

Definition at line 554 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 926 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::haAngleExp

Definition at line 900 of file SimParameters.h.

BigReal SimParameters::hgroupCutoff

Definition at line 844 of file SimParameters.h.

int SimParameters::hybridGroupSize

Definition at line 134 of file SimParameters.h.

Bool SimParameters::HydrogenBonds

Definition at line 890 of file SimParameters.h.

Bool SimParameters::ignoreMass

Definition at line 841 of file SimParameters.h.

int SimParameters::IMDfreq

Definition at line 912 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::IMDignore

Definition at line 915 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDignoreForces

Definition at line 917 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDon

Definition at line 910 of file SimParameters.h.

Referenced by Controller::printEnergies().

int SimParameters::IMDport

Definition at line 911 of file SimParameters.h.

Referenced by GlobalMasterIMD::GlobalMasterIMD().

int SimParameters::IMDwait

Definition at line 913 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 498 of file SimParameters.h.

BigReal SimParameters::kappa

Definition at line 497 of file SimParameters.h.

Bool SimParameters::langevin_useBAOAB

Definition at line 544 of file SimParameters.h.

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

BigReal SimParameters::langevinDamping

Definition at line 542 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinHydrogen

Definition at line 543 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::langevinOn

Definition at line 540 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 539 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::langevinPistonBarrier

Definition at line 639 of file SimParameters.h.

Referenced by Controller::langevinPiston1().

BigReal SimParameters::langevinPistonDecay

Definition at line 642 of file SimParameters.h.

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

Bool SimParameters::langevinPistonOn

Definition at line 638 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 641 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTarget

Definition at line 640 of file SimParameters.h.

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

BigReal SimParameters::langevinPistonTemp

Definition at line 643 of file SimParameters.h.

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

BigReal SimParameters::langevinTemp

Definition at line 541 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 504 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 427 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 426 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 429 of file SimParameters.h.

Bool SimParameters::lesReduceTemp

Definition at line 428 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 970 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 838 of file SimParameters.h.

BigReal SimParameters::loweAndersenCutoff

Definition at line 551 of file SimParameters.h.

Bool SimParameters::loweAndersenOn

Definition at line 548 of file SimParameters.h.

Referenced by Sequencer::integrate().

BigReal SimParameters::loweAndersenRate

Definition at line 550 of file SimParameters.h.

BigReal SimParameters::loweAndersenTemp

Definition at line 549 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::mallocTest

Definition at line 947 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 878 of file SimParameters.h.

BigReal SimParameters::maximumMove

Definition at line 766 of file SimParameters.h.

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

int SimParameters::maxPairPart

Definition at line 866 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 864 of file SimParameters.h.

Bool SimParameters::mergeCrossterms

Definition at line 830 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 978 of file SimParameters.h.

int SimParameters::mic_hostSplit

Definition at line 973 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p1

Definition at line 975 of file SimParameters.h.

int SimParameters::mic_numParts_pair_p2

Definition at line 976 of file SimParameters.h.

int SimParameters::mic_numParts_self_p1

Definition at line 974 of file SimParameters.h.

int SimParameters::mic_singleKernel

Definition at line 979 of file SimParameters.h.

int SimParameters::mic_unloadMICPEs

Definition at line 977 of file SimParameters.h.

int SimParameters::minAtomsPerPatch

Definition at line 876 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

BigReal SimParameters::minBabyStep

Definition at line 763 of file SimParameters.h.

Bool SimParameters::minimizeCGOn

Definition at line 760 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::minimizeOn

Definition at line 765 of file SimParameters.h.

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

BigReal SimParameters::minLineGoal

Definition at line 764 of file SimParameters.h.

Referenced by Controller::minimize().

BigReal SimParameters::minTinyStep

Definition at line 762 of file SimParameters.h.

Bool SimParameters::minVerbose

Definition at line 761 of file SimParameters.h.

Referenced by Controller::minimize().

Bool SimParameters::miscForcesOn

Definition at line 532 of file SimParameters.h.

int SimParameters::mollyIter

Definition at line 848 of file SimParameters.h.

int SimParameters::mollyOn

Definition at line 846 of file SimParameters.h.

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

BigReal SimParameters::mollyTol

Definition at line 847 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 686 of file SimParameters.h.

int SimParameters::MSMBlockSizeX

Definition at line 696 of file SimParameters.h.

int SimParameters::MSMBlockSizeY

Definition at line 697 of file SimParameters.h.

int SimParameters::MSMBlockSizeZ

Definition at line 698 of file SimParameters.h.

BigReal SimParameters::MSMGridSpacing

Definition at line 700 of file SimParameters.h.

int SimParameters::MSMLevels

Definition at line 692 of file SimParameters.h.

Bool SimParameters::MSMOn

Definition at line 679 of file SimParameters.h.

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

BigReal SimParameters::MSMPadding

Definition at line 702 of file SimParameters.h.

int SimParameters::MSMQuality

Definition at line 682 of file SimParameters.h.

Bool SimParameters::MsmSerialOn

Definition at line 715 of file SimParameters.h.

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

int SimParameters::MSMSplit

Definition at line 689 of file SimParameters.h.

BigReal SimParameters::MSMxmax

Definition at line 709 of file SimParameters.h.

BigReal SimParameters::MSMxmin

Definition at line 708 of file SimParameters.h.

BigReal SimParameters::MSMymax

Definition at line 711 of file SimParameters.h.

BigReal SimParameters::MSMymin

Definition at line 710 of file SimParameters.h.

BigReal SimParameters::MSMzmax

Definition at line 713 of file SimParameters.h.

BigReal SimParameters::MSMzmin

Definition at line 712 of file SimParameters.h.

MTSChoices SimParameters::MTSAlgorithm

Definition at line 835 of file SimParameters.h.

Referenced by Sequencer::integrate().

int SimParameters::multigratorNoseHooverChainLength

Definition at line 652 of file SimParameters.h.

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

Bool SimParameters::multigratorOn

Definition at line 645 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 648 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureRelaxationTime

Definition at line 647 of file SimParameters.h.

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

BigReal SimParameters::multigratorPressureTarget

Definition at line 646 of file SimParameters.h.

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

int SimParameters::multigratorTemperatureFreq

Definition at line 651 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureRelaxationTime

Definition at line 650 of file SimParameters.h.

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

BigReal SimParameters::multigratorTemperatureTarget

Definition at line 649 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 ComputeQMMgr::recvPntChrg(), and scriptSet().

Bool SimParameters::noPatchesOnOne

Definition at line 174 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnOutputPEs

Definition at line 173 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

Bool SimParameters::noPatchesOnZero

Definition at line 172 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::numAtomsPair

Definition at line 872 of file SimParameters.h.

int SimParameters::numAtomsPair2

Definition at line 874 of file SimParameters.h.

int SimParameters::numAtomsSelf

Definition at line 868 of file SimParameters.h.

int SimParameters::numAtomsSelf2

Definition at line 870 of file SimParameters.h.

int SimParameters::numinputprocs

Definition at line 958 of file SimParameters.h.

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

int SimParameters::numoutputprocs

Definition at line 965 of file SimParameters.h.

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

int SimParameters::numoutputwrts

Definition at line 966 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 824 of file SimParameters.h.

int SimParameters::outputEnergies

Definition at line 815 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 818 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 880 of file SimParameters.h.

Referenced by WorkDistrib::createAtomLists().

int SimParameters::outputPressure

Definition at line 827 of file SimParameters.h.

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

int SimParameters::outputTiming

Definition at line 821 of file SimParameters.h.

Referenced by Controller::printTiming().

int SimParameters::pairInteractionGroup1

Definition at line 518 of file SimParameters.h.

int SimParameters::pairInteractionGroup2

Definition at line 519 of file SimParameters.h.

Bool SimParameters::pairInteractionOn

Definition at line 517 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 520 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 732 of file SimParameters.h.

BigReal SimParameters::PMEEwaldCoefficient

Definition at line 723 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::PMEGridSizeX

Definition at line 725 of file SimParameters.h.

int SimParameters::PMEGridSizeY

Definition at line 726 of file SimParameters.h.

int SimParameters::PMEGridSizeZ

Definition at line 727 of file SimParameters.h.

BigReal SimParameters::PMEGridSpacing

Definition at line 728 of file SimParameters.h.

int SimParameters::PMEInterpOrder

Definition at line 724 of file SimParameters.h.

int SimParameters::PMEMinPoints

Definition at line 731 of file SimParameters.h.

int SimParameters::PMEMinSlices

Definition at line 730 of file SimParameters.h.

Bool SimParameters::PMEOffload

Definition at line 740 of file SimParameters.h.

Referenced by ComputeNonbondedCUDA::ComputeNonbondedCUDA().

Bool SimParameters::PMEOn

Definition at line 721 of file SimParameters.h.

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

int SimParameters::PMEPencils

Definition at line 733 of file SimParameters.h.

int SimParameters::PMEPencilsX

Definition at line 734 of file SimParameters.h.

int SimParameters::PMEPencilsXLayout

Definition at line 738 of file SimParameters.h.

int SimParameters::PMEPencilsY

Definition at line 735 of file SimParameters.h.

int SimParameters::PMEPencilsYLayout

Definition at line 737 of file SimParameters.h.

int SimParameters::PMEPencilsZ

Definition at line 736 of file SimParameters.h.

int SimParameters::PMEProcessors

Definition at line 729 of file SimParameters.h.

int SimParameters::PMESendOrder

Definition at line 739 of file SimParameters.h.

BigReal SimParameters::PMETolerance

Definition at line 722 of file SimParameters.h.

int SimParameters::pressureProfileAtomTypes

Definition at line 659 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 660 of file SimParameters.h.

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

int SimParameters::pressureProfileEwaldX

Definition at line 661 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldY

Definition at line 662 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileEwaldZ

Definition at line 663 of file SimParameters.h.

Referenced by ComputeEwald::ComputeEwald().

int SimParameters::pressureProfileFreq

Definition at line 658 of file SimParameters.h.

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

Bool SimParameters::pressureProfileOn

Definition at line 656 of file SimParameters.h.

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

int SimParameters::pressureProfileSlabs

Definition at line 657 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 489 of file SimParameters.h.

Referenced by Sequencer::submitMinimizeReductions().

Bool SimParameters::printExclusions

Definition at line 948 of file SimParameters.h.

int SimParameters::proxyRecvSpanningTree

Definition at line 952 of file SimParameters.h.

Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().

int SimParameters::proxySendSpanningTree

Definition at line 951 of file SimParameters.h.

Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().

int SimParameters::proxyTreeBranchFactor

Definition at line 954 of file SimParameters.h.

Referenced by Node::startup().

char SimParameters::qmBaseDir[256]

Definition at line 447 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmBondColumn[16]

Definition at line 457 of file SimParameters.h.

Bool SimParameters::qmBondDist

Definition at line 458 of file SimParameters.h.

Bool SimParameters::qmBondOn

Definition at line 456 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

int SimParameters::qmBondScheme

Definition at line 462 of file SimParameters.h.

char SimParameters::qmBondSchemeS[16]

Definition at line 461 of file SimParameters.h.

int SimParameters::qmBondValType

Definition at line 459 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmBondValueTypeS[16]

Definition at line 460 of file SimParameters.h.

Bool SimParameters::qmChrgFromPSF

Definition at line 441 of file SimParameters.h.

int SimParameters::qmChrgMode

Definition at line 445 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmChrgModeS[16]

Definition at line 444 of file SimParameters.h.

char SimParameters::qmColumn[16]

Definition at line 446 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmCSMD

Definition at line 482 of file SimParameters.h.

char SimParameters::qmCSMDFile[128]

Definition at line 483 of file SimParameters.h.

Bool SimParameters::qmCustomPCSel

Definition at line 474 of file SimParameters.h.

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

Bool SimParameters::qmElecEmbed

Definition at line 472 of file SimParameters.h.

int SimParameters::qmEnergyOutFreq

Definition at line 485 of file SimParameters.h.

Referenced by ComputeQMMgr::storeQMRes().

char SimParameters::qmExecPath[256]

Definition at line 442 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmForcesOn

Definition at line 438 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 452 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmLSSFreq

Definition at line 477 of file SimParameters.h.

int SimParameters::qmLSSMode

Definition at line 480 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

char SimParameters::qmLSSModeS[16]

Definition at line 479 of file SimParameters.h.

Bool SimParameters::qmLSSOn

Definition at line 476 of file SimParameters.h.

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

char SimParameters::qmLSSResname[5]

Definition at line 478 of file SimParameters.h.

Bool SimParameters::qmMOPACAddConfigChrg

Definition at line 454 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmNoPC

Definition at line 471 of file SimParameters.h.

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

int SimParameters::qmOutFreq

Definition at line 486 of file SimParameters.h.

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

char SimParameters::qmParamPDB[128]

Definition at line 439 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::qmParamPDBDefined

Definition at line 440 of file SimParameters.h.

Referenced by NamdState::loadStructure().

int SimParameters::qmPCScheme

Definition at line 467 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSchemeS[16]

Definition at line 466 of file SimParameters.h.

int SimParameters::qmPCSelFreq

Definition at line 473 of file SimParameters.h.

Referenced by Molecule::prepare_qm().

Bool SimParameters::qmPCSwitchOn

Definition at line 463 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmPCSwitchType

Definition at line 465 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

char SimParameters::qmPCSwitchTypeS[16]

Definition at line 464 of file SimParameters.h.

int SimParameters::qmPosOutFreq

Definition at line 487 of file SimParameters.h.

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

char SimParameters::qmPrepProc[256]

Definition at line 450 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmPrepProcOn

Definition at line 451 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmReplaceAll

Definition at line 453 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::qmSecProc[256]

Definition at line 448 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

Bool SimParameters::qmSecProcOn

Definition at line 449 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPntChrg().

int SimParameters::qmSimsPerNode

Definition at line 468 of file SimParameters.h.

Referenced by ComputeQMMgr::recvPartQM().

char SimParameters::qmSoftware[128]

Definition at line 443 of file SimParameters.h.

Bool SimParameters::qmVDW

Definition at line 470 of file SimParameters.h.

unsigned int SimParameters::randomSeed

Definition at line 668 of file SimParameters.h.

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

Bool SimParameters::readExclusions

Definition at line 922 of file SimParameters.h.

Referenced by buildExclusions().

int SimParameters::reassignFreq

Definition at line 613 of file SimParameters.h.

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

BigReal SimParameters::reassignHold

Definition at line 616 of file SimParameters.h.

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

BigReal SimParameters::reassignIncr

Definition at line 615 of file SimParameters.h.

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

BigReal SimParameters::reassignTemp

Definition at line 614 of file SimParameters.h.

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

Bool SimParameters::replicaUniformPatchGrids

Definition at line 882 of file SimParameters.h.

Referenced by WorkDistrib::patchMapInit().

int SimParameters::rescaleFreq

Definition at line 565 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 566 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 850 of file SimParameters.h.

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

int SimParameters::rigidDie

Definition at line 855 of file SimParameters.h.

int SimParameters::rigidIter

Definition at line 854 of file SimParameters.h.

BigReal SimParameters::rigidTol

Definition at line 853 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 932 of file SimParameters.h.

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

BigReal SimParameters::scriptArg2

Definition at line 933 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg3

Definition at line 934 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg4

Definition at line 935 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::scriptArg5

Definition at line 936 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::scriptIntArg1

Definition at line 937 of file SimParameters.h.

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

int SimParameters::scriptIntArg2

Definition at line 938 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::scriptStringArg1[128]

Definition at line 939 of file SimParameters.h.

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

char SimParameters::scriptStringArg2[128]

Definition at line 940 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 495 of file SimParameters.h.

int SimParameters::sphericalBCexp1

Definition at line 778 of file SimParameters.h.

int SimParameters::sphericalBCexp2

Definition at line 779 of file SimParameters.h.

BigReal SimParameters::sphericalBCk1

Definition at line 772 of file SimParameters.h.

BigReal SimParameters::sphericalBCk2

Definition at line 774 of file SimParameters.h.

Bool SimParameters::sphericalBCOn

Definition at line 769 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

BigReal SimParameters::sphericalBCr1

Definition at line 776 of file SimParameters.h.

BigReal SimParameters::sphericalBCr2

Definition at line 777 of file SimParameters.h.

zVector SimParameters::sphericalCenter

Definition at line 771 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 843 of file SimParameters.h.

Bool SimParameters::staticAtomAssignment

Definition at line 881 of file SimParameters.h.

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

Bool SimParameters::statsOn

Definition at line 861 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 806 of file SimParameters.h.

Referenced by scriptSet().

char SimParameters::stirFilename[128]

Definition at line 801 of file SimParameters.h.

BigReal SimParameters::stirK

Definition at line 805 of file SimParameters.h.

Bool SimParameters::stirOn

Definition at line 800 of file SimParameters.h.

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

zVector SimParameters::stirPivot

Definition at line 807 of file SimParameters.h.

Referenced by scriptSet().

BigReal SimParameters::stirStartingTheta

Definition at line 803 of file SimParameters.h.

BigReal SimParameters::stirVel

Definition at line 804 of file SimParameters.h.

Bool SimParameters::storeComputeMap

Definition at line 969 of file SimParameters.h.

zVector SimParameters::strainRate

Definition at line 665 of file SimParameters.h.

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

zVector SimParameters::strainRate2

Definition at line 666 of file SimParameters.h.

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

BigReal SimParameters::surface_tension

Definition at line 505 of file SimParameters.h.

BigReal SimParameters::surfaceTensionTarget

Definition at line 654 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 530 of file SimParameters.h.

Referenced by scriptSet().

Bool SimParameters::tclBCOn

Definition at line 528 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

char* SimParameters::tclBCScript

Definition at line 529 of file SimParameters.h.

Referenced by receive_SimParameters(), and send_SimParameters().

Bool SimParameters::tclForcesOn

Definition at line 524 of file SimParameters.h.

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

Bool SimParameters::tclIsThreaded

Definition at line 526 of file SimParameters.h.

Bool SimParameters::tCoupleOn

Definition at line 561 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 563 of file SimParameters.h.

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

Bool SimParameters::testOn

Definition at line 859 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 863 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 893 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 942 of file SimParameters.h.

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

Bool SimParameters::useConstantArea

Definition at line 624 of file SimParameters.h.

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

Bool SimParameters::useConstantRatio

Definition at line 625 of file SimParameters.h.

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

Bool SimParameters::useCUDA2

Definition at line 744 of file SimParameters.h.

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

Bool SimParameters::useDPME

Definition at line 742 of file SimParameters.h.

Referenced by WorkDistrib::mapComputes().

Bool SimParameters::useFlexibleCell

Definition at line 623 of file SimParameters.h.

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

Bool SimParameters::useGroupPressure

Definition at line 618 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 747 of file SimParameters.h.

Bool SimParameters::useOptPME

Definition at line 746 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 945 of file SimParameters.h.

Referenced by NamdState::loadStructure().

Bool SimParameters::usePMECUDA

Definition at line 743 of file SimParameters.h.

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

Bool SimParameters::useSettle

Definition at line 857 of file SimParameters.h.

Bool SimParameters::vdwForceSwitching

Definition at line 230 of file SimParameters.h.

Bool SimParameters::vdwGeometricSigma

Definition at line 929 of file SimParameters.h.

BigReal SimParameters::vdwscale14

Definition at line 923 of file SimParameters.h.

Referenced by NamdState::loadStructure().

char SimParameters::velDcdFilename[128]

Definition at line 202 of file SimParameters.h.

Referenced by scriptSet().

int SimParameters::velDcdFrequency

Definition at line 194 of file SimParameters.h.

Bool SimParameters::verboseTopology

Definition at line 154 of file SimParameters.h.

int SimParameters::watmodel

Definition at line 109 of file SimParameters.h.

Bool SimParameters::wrapAll

Definition at line 183 of file SimParameters.h.

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

Bool SimParameters::wrapNearest

Definition at line 184 of file SimParameters.h.

Referenced by ParallelIOMgr::recvFinalClusterCoor().

Bool SimParameters::wrapWater

Definition at line 182 of file SimParameters.h.

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

char SimParameters::xstFilename[128]

Definition at line 204 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

int SimParameters::xstFrequency

Definition at line 198 of file SimParameters.h.

Referenced by Controller::outputExtendedSystem().

Bool SimParameters::zeroMomentum

Definition at line 180 of file SimParameters.h.

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

Bool SimParameters::zeroMomentumAlt

Definition at line 181 of file SimParameters.h.

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


The documentation for this class was generated from the following files:
Generated on Sat Feb 24 01:17:22 2018 for NAMD by  doxygen 1.4.7