--- branches/development/src/integrators/RNEMD.cpp 2012/05/24 20:59:54 1723 +++ branches/development/src/rnemd/RNEMD.cpp 2013/05/17 17:10:11 1876 @@ -35,12 +35,15 @@ * * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). - * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). * [4] Vardeman & Gezelter, in progress (2009). */ #include -#include "integrators/RNEMD.hpp" +#include +#include + +#include "rnemd/RNEMD.hpp" #include "math/Vector3.hpp" #include "math/Vector.hpp" #include "math/SquareMatrix3.hpp" @@ -49,290 +52,573 @@ #include "primitives/StuntDouble.hpp" #include "utils/PhysicalConstants.hpp" #include "utils/Tuple.hpp" - -#ifndef IS_MPI -#include "math/SeqRandNumGen.hpp" -#else -#include "math/ParallelRandNumGen.hpp" +#include "brains/Thermo.hpp" +#include "math/ConvexHull.hpp" +#ifdef IS_MPI #include #endif +#ifdef _MSC_VER +#define isnan(x) _isnan((x)) +#define isinf(x) (!_finite(x) && !_isnan(x)) +#endif + #define HONKING_LARGE_VALUE 1.0e10 using namespace std; namespace OpenMD { RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), + evaluatorA_(info), seleManA_(info), + commonA_(info), evaluatorB_(info), + seleManB_(info), commonB_(info), + hasData_(false), hasDividingArea_(false), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { + trialCount_ = 0; failTrialCount_ = 0; failRootCount_ = 0; - int seedValue; - Globals * simParams = info->getSimParams(); + Globals* simParams = info->getSimParams(); + RNEMDParameters* rnemdParams = simParams->getRNEMDParameters(); - stringToEnumMap_["KineticSwap"] = rnemdKineticSwap; - stringToEnumMap_["KineticScale"] = rnemdKineticScale; - stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM; - stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM; - stringToEnumMap_["PxScale"] = rnemdPxScale; - stringToEnumMap_["PyScale"] = rnemdPyScale; - stringToEnumMap_["PzScale"] = rnemdPzScale; - stringToEnumMap_["Px"] = rnemdPx; - stringToEnumMap_["Py"] = rnemdPy; - stringToEnumMap_["Pz"] = rnemdPz; - stringToEnumMap_["ShiftScaleV"] = rnemdShiftScaleV; - stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM; - stringToEnumMap_["Unknown"] = rnemdUnknown; + doRNEMD_ = rnemdParams->getUseRNEMD(); + if (!doRNEMD_) return; - rnemdObjectSelection_ = simParams->getRNEMD_objectSelection(); - evaluator_.loadScriptString(rnemdObjectSelection_); - seleMan_.setSelectionSet(evaluator_.evaluate()); + stringToMethod_["Swap"] = rnemdSwap; + stringToMethod_["NIVS"] = rnemdNIVS; + stringToMethod_["VSS"] = rnemdVSS; - // do some sanity checking + stringToFluxType_["KE"] = rnemdKE; + stringToFluxType_["Px"] = rnemdPx; + stringToFluxType_["Py"] = rnemdPy; + stringToFluxType_["Pz"] = rnemdPz; + stringToFluxType_["Pvector"] = rnemdPvector; + stringToFluxType_["Lx"] = rnemdLx; + stringToFluxType_["Ly"] = rnemdLy; + stringToFluxType_["Lz"] = rnemdLz; + stringToFluxType_["Lvector"] = rnemdLvector; + stringToFluxType_["KE+Px"] = rnemdKePx; + stringToFluxType_["KE+Py"] = rnemdKePy; + stringToFluxType_["KE+Pvector"] = rnemdKePvector; + stringToFluxType_["KE+Lx"] = rnemdKeLx; + stringToFluxType_["KE+Ly"] = rnemdKeLy; + stringToFluxType_["KE+Lz"] = rnemdKeLz; + stringToFluxType_["KE+Lvector"] = rnemdKeLvector; - int selectionCount = seleMan_.getSelectionCount(); - int nIntegrable = info->getNGlobalIntegrableObjects(); + runTime_ = simParams->getRunTime(); + statusTime_ = simParams->getStatusTime(); - if (selectionCount > nIntegrable) { + const string methStr = rnemdParams->getMethod(); + bool hasFluxType = rnemdParams->haveFluxType(); + + rnemdObjectSelection_ = rnemdParams->getObjectSelection(); + + string fluxStr; + if (hasFluxType) { + fluxStr = rnemdParams->getFluxType(); + } else { sprintf(painCave.errMsg, - "RNEMD: The current RNEMD_objectSelection,\n" - "\t\t%s\n" - "\thas resulted in %d selected objects. However,\n" - "\tthe total number of integrable objects in the system\n" - "\tis only %d. This is almost certainly not what you want\n" - "\tto do. A likely cause of this is forgetting the _RB_0\n" - "\tselector in the selection script!\n", - rnemdObjectSelection_.c_str(), - selectionCount, nIntegrable); - painCave.isFatal = 0; - painCave.severity = OPENMD_WARNING; + "RNEMD: No fluxType was set in the md file. This parameter,\n" + "\twhich must be one of the following values:\n" + "\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n" + "\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n" + "\tmust be set to use RNEMD\n"); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; simError(); } + + bool hasKineticFlux = rnemdParams->haveKineticFlux(); + bool hasMomentumFlux = rnemdParams->haveMomentumFlux(); + bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector(); + bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux(); + bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector(); + hasSelectionA_ = rnemdParams->haveSelectionA(); + hasSelectionB_ = rnemdParams->haveSelectionB(); + bool hasSlabWidth = rnemdParams->haveSlabWidth(); + bool hasSlabACenter = rnemdParams->haveSlabACenter(); + bool hasSlabBCenter = rnemdParams->haveSlabBCenter(); + bool hasSphereARadius = rnemdParams->haveSphereARadius(); + hasSphereBRadius_ = rnemdParams->haveSphereBRadius(); + bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin(); + bool hasOutputFileName = rnemdParams->haveOutputFileName(); + bool hasOutputFields = rnemdParams->haveOutputFields(); - const string st = simParams->getRNEMD_exchangeType(); + map::iterator i; + i = stringToMethod_.find(methStr); + if (i != stringToMethod_.end()) + rnemdMethod_ = i->second; + else { + sprintf(painCave.errMsg, + "RNEMD: The current method,\n" + "\t\t%s is not one of the recognized\n" + "\texchange methods: Swap, NIVS, or VSS\n", + methStr.c_str()); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; + simError(); + } - map::iterator i; - i = stringToEnumMap_.find(st); - rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second; - if (rnemdType_ == rnemdUnknown) { + map::iterator j; + j = stringToFluxType_.find(fluxStr); + if (j != stringToFluxType_.end()) + rnemdFluxType_ = j->second; + else { sprintf(painCave.errMsg, - "RNEMD: The current RNEMD_exchangeType,\n" + "RNEMD: The current fluxType,\n" "\t\t%s\n" - "\tis not one of the recognized exchange types.\n", - st.c_str()); + "\tis not one of the recognized flux types.\n", + fluxStr.c_str()); painCave.isFatal = 1; painCave.severity = OPENMD_ERROR; simError(); } - - outputTemp_ = false; - if (simParams->haveRNEMD_outputTemperature()) { - outputTemp_ = simParams->getRNEMD_outputTemperature(); - } else if ((rnemdType_ == rnemdKineticSwap) || - (rnemdType_ == rnemdKineticScale) || - (rnemdType_ == rnemdKineticScaleVAM) || - (rnemdType_ == rnemdKineticScaleAM)) { - outputTemp_ = true; - } - outputVx_ = false; - if (simParams->haveRNEMD_outputVx()) { - outputVx_ = simParams->getRNEMD_outputVx(); - } else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) { - outputVx_ = true; - } - outputVy_ = false; - if (simParams->haveRNEMD_outputVy()) { - outputVy_ = simParams->getRNEMD_outputVy(); - } else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) { - outputVy_ = true; - } - output3DTemp_ = false; - if (simParams->haveRNEMD_outputXyzTemperature()) { - output3DTemp_ = simParams->getRNEMD_outputXyzTemperature(); - } - outputRotTemp_ = false; - if (simParams->haveRNEMD_outputRotTemperature()) { - outputRotTemp_ = simParams->getRNEMD_outputRotTemperature(); - } -#ifdef IS_MPI - if (worldRank == 0) { -#endif - - //may have rnemdWriter separately - string rnemdFileName; - - if (outputTemp_) { - rnemdFileName = "temperature.log"; - tempLog_.open(rnemdFileName.c_str()); + bool methodFluxMismatch = false; + bool hasCorrectFlux = false; + switch(rnemdMethod_) { + case rnemdSwap: + switch (rnemdFluxType_) { + case rnemdKE: + hasCorrectFlux = hasKineticFlux; + break; + case rnemdPx: + case rnemdPy: + case rnemdPz: + hasCorrectFlux = hasMomentumFlux; + break; + default : + methodFluxMismatch = true; + break; } - if (outputVx_) { - rnemdFileName = "velocityX.log"; - vxzLog_.open(rnemdFileName.c_str()); + break; + case rnemdNIVS: + switch (rnemdFluxType_) { + case rnemdKE: + case rnemdRotKE: + case rnemdFullKE: + hasCorrectFlux = hasKineticFlux; + break; + case rnemdPx: + case rnemdPy: + case rnemdPz: + hasCorrectFlux = hasMomentumFlux; + break; + case rnemdKePx: + case rnemdKePy: + hasCorrectFlux = hasMomentumFlux && hasKineticFlux; + break; + default: + methodFluxMismatch = true; + break; } - if (outputVy_) { - rnemdFileName = "velocityY.log"; - vyzLog_.open(rnemdFileName.c_str()); + break; + case rnemdVSS: + switch (rnemdFluxType_) { + case rnemdKE: + case rnemdRotKE: + case rnemdFullKE: + hasCorrectFlux = hasKineticFlux; + break; + case rnemdPx: + case rnemdPy: + case rnemdPz: + hasCorrectFlux = hasMomentumFlux; + break; + case rnemdLx: + case rnemdLy: + case rnemdLz: + hasCorrectFlux = hasAngularMomentumFlux; + break; + case rnemdPvector: + hasCorrectFlux = hasMomentumFluxVector; + break; + case rnemdLvector: + hasCorrectFlux = hasAngularMomentumFluxVector; + break; + case rnemdKePx: + case rnemdKePy: + hasCorrectFlux = hasMomentumFlux && hasKineticFlux; + break; + case rnemdKeLx: + case rnemdKeLy: + case rnemdKeLz: + hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux; + break; + case rnemdKePvector: + hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux; + break; + case rnemdKeLvector: + hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux; + break; + default: + methodFluxMismatch = true; + break; } + default: + break; + } - if (output3DTemp_) { - rnemdFileName = "temperatureX.log"; - xTempLog_.open(rnemdFileName.c_str()); - rnemdFileName = "temperatureY.log"; - yTempLog_.open(rnemdFileName.c_str()); - rnemdFileName = "temperatureZ.log"; - zTempLog_.open(rnemdFileName.c_str()); + if (methodFluxMismatch) { + sprintf(painCave.errMsg, + "RNEMD: The current method,\n" + "\t\t%s\n" + "\tcannot be used with the current flux type, %s\n", + methStr.c_str(), fluxStr.c_str()); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; + simError(); + } + if (!hasCorrectFlux) { + sprintf(painCave.errMsg, + "RNEMD: The current method, %s, and flux type, %s,\n" + "\tdid not have the correct flux value specified. Options\n" + "\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n" + "\tmomentumFluxVector, and angularMomentumFluxVector.\n", + methStr.c_str(), fluxStr.c_str()); + painCave.isFatal = 1; + painCave.severity = OPENMD_ERROR; + simError(); + } + + if (hasKineticFlux) { + // convert the kcal / mol / Angstroms^2 / fs values in the md file + // into amu / fs^3: + kineticFlux_ = rnemdParams->getKineticFlux() + * PhysicalConstants::energyConvert; + } else { + kineticFlux_ = 0.0; + } + if (hasMomentumFluxVector) { + momentumFluxVector_ = rnemdParams->getMomentumFluxVector(); + } else { + momentumFluxVector_ = V3Zero; + if (hasMomentumFlux) { + RealType momentumFlux = rnemdParams->getMomentumFlux(); + switch (rnemdFluxType_) { + case rnemdPx: + momentumFluxVector_.x() = momentumFlux; + break; + case rnemdPy: + momentumFluxVector_.y() = momentumFlux; + break; + case rnemdPz: + momentumFluxVector_.z() = momentumFlux; + break; + case rnemdKePx: + momentumFluxVector_.x() = momentumFlux; + break; + case rnemdKePy: + momentumFluxVector_.y() = momentumFlux; + break; + default: + break; + } } - if (outputRotTemp_) { - rnemdFileName = "temperatureR.log"; - rotTempLog_.open(rnemdFileName.c_str()); + if (hasAngularMomentumFluxVector) { + angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector(); + } else { + angularMomentumFluxVector_ = V3Zero; + if (hasAngularMomentumFlux) { + RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux(); + switch (rnemdFluxType_) { + case rnemdLx: + angularMomentumFluxVector_.x() = angularMomentumFlux; + break; + case rnemdLy: + angularMomentumFluxVector_.y() = angularMomentumFlux; + break; + case rnemdLz: + angularMomentumFluxVector_.z() = angularMomentumFlux; + break; + case rnemdKeLx: + angularMomentumFluxVector_.x() = angularMomentumFlux; + break; + case rnemdKeLy: + angularMomentumFluxVector_.y() = angularMomentumFlux; + break; + case rnemdKeLz: + angularMomentumFluxVector_.z() = angularMomentumFlux; + break; + default: + break; + } + } } -#ifdef IS_MPI - } -#endif - - set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime()); - set_RNEMD_nBins(simParams->getRNEMD_nBins()); - midBin_ = nBins_ / 2; - if (simParams->haveRNEMD_binShift()) { - if (simParams->getRNEMD_binShift()) { - zShift_ = 0.5 / (RealType)(nBins_); + if (hasCoordinateOrigin) { + coordinateOrigin_ = rnemdParams->getCoordinateOrigin(); } else { - zShift_ = 0.0; + coordinateOrigin_ = V3Zero; } - } else { - zShift_ = 0.0; - } - //cerr << "I shift slabs by " << zShift_ << " Lz\n"; - //shift slabs by half slab width, maybe useful in heterogeneous systems - //set to 0.0 if not using it; N/A in status output yet - if (simParams->haveRNEMD_logWidth()) { - set_RNEMD_logWidth(simParams->getRNEMD_logWidth()); - /*arbitary rnemdLogWidth_, no checking; - if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) { - cerr << "WARNING! RNEMD_logWidth has abnormal value!\n"; - cerr << "Automaically set back to default.\n"; - rnemdLogWidth_ = nBins_; - }*/ - } else { - set_RNEMD_logWidth(nBins_); - } - tempHist_.resize(rnemdLogWidth_, 0.0); - tempCount_.resize(rnemdLogWidth_, 0); - pxzHist_.resize(rnemdLogWidth_, 0.0); - //vxzCount_.resize(rnemdLogWidth_, 0); - pyzHist_.resize(rnemdLogWidth_, 0.0); - //vyzCount_.resize(rnemdLogWidth_, 0); - mHist_.resize(rnemdLogWidth_, 0.0); - xTempHist_.resize(rnemdLogWidth_, 0.0); - yTempHist_.resize(rnemdLogWidth_, 0.0); - zTempHist_.resize(rnemdLogWidth_, 0.0); - xyzTempCount_.resize(rnemdLogWidth_, 0); - rotTempHist_.resize(rnemdLogWidth_, 0.0); - rotTempCount_.resize(rnemdLogWidth_, 0); + // do some sanity checking - set_RNEMD_exchange_total(0.0); - if (simParams->haveRNEMD_targetFlux()) { - set_RNEMD_target_flux(simParams->getRNEMD_targetFlux()); - } else { - set_RNEMD_target_flux(0.0); - } - if (simParams->haveRNEMD_targetJzKE()) { - set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE()); - } else { - set_RNEMD_target_JzKE(0.0); - } - if (simParams->haveRNEMD_targetJzpx()) { - set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx()); - } else { - set_RNEMD_target_jzpx(0.0); - } - jzp_.x() = targetJzpx_; - njzp_.x() = -targetJzpx_; - if (simParams->haveRNEMD_targetJzpy()) { - set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy()); - } else { - set_RNEMD_target_jzpy(0.0); - } - jzp_.y() = targetJzpy_; - njzp_.y() = -targetJzpy_; - if (simParams->haveRNEMD_targetJzpz()) { - set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz()); - } else { - set_RNEMD_target_jzpz(0.0); - } - jzp_.z() = targetJzpz_; - njzp_.z() = -targetJzpz_; + int selectionCount = seleMan_.getSelectionCount(); -#ifndef IS_MPI - if (simParams->haveSeed()) { - seedValue = simParams->getSeed(); - randNumGen_ = new SeqRandNumGen(seedValue); - }else { - randNumGen_ = new SeqRandNumGen(); - } -#else - if (simParams->haveSeed()) { - seedValue = simParams->getSeed(); - randNumGen_ = new ParallelRandNumGen(seedValue); - }else { - randNumGen_ = new ParallelRandNumGen(); - } -#endif + int nIntegrable = info->getNGlobalIntegrableObjects(); + + if (selectionCount > nIntegrable) { + sprintf(painCave.errMsg, + "RNEMD: The current objectSelection,\n" + "\t\t%s\n" + "\thas resulted in %d selected objects. However,\n" + "\tthe total number of integrable objects in the system\n" + "\tis only %d. This is almost certainly not what you want\n" + "\tto do. A likely cause of this is forgetting the _RB_0\n" + "\tselector in the selection script!\n", + rnemdObjectSelection_.c_str(), + selectionCount, nIntegrable); + painCave.isFatal = 0; + painCave.severity = OPENMD_WARNING; + simError(); + } + + areaAccumulator_ = new Accumulator(); + + nBins_ = rnemdParams->getOutputBins(); + binWidth_ = rnemdParams->getOutputBinWidth(); + + data_.resize(RNEMD::ENDINDEX); + OutputData z; + z.units = "Angstroms"; + z.title = "Z"; + z.dataType = "RealType"; + z.accumulator.reserve(nBins_); + for (int i = 0; i < nBins_; i++) + z.accumulator.push_back( new Accumulator() ); + data_[Z] = z; + outputMap_["Z"] = Z; + + OutputData r; + r.units = "Angstroms"; + r.title = "R"; + r.dataType = "RealType"; + r.accumulator.reserve(nBins_); + for (int i = 0; i < nBins_; i++) + r.accumulator.push_back( new Accumulator() ); + data_[R] = r; + outputMap_["R"] = R; + + OutputData temperature; + temperature.units = "K"; + temperature.title = "Temperature"; + temperature.dataType = "RealType"; + temperature.accumulator.reserve(nBins_); + for (int i = 0; i < nBins_; i++) + temperature.accumulator.push_back( new Accumulator() ); + data_[TEMPERATURE] = temperature; + outputMap_["TEMPERATURE"] = TEMPERATURE; + + OutputData velocity; + velocity.units = "angstroms/fs"; + velocity.title = "Velocity"; + velocity.dataType = "Vector3d"; + velocity.accumulator.reserve(nBins_); + for (int i = 0; i < nBins_; i++) + velocity.accumulator.push_back( new VectorAccumulator() ); + data_[VELOCITY] = velocity; + outputMap_["VELOCITY"] = VELOCITY; + + OutputData angularVelocity; + angularVelocity.units = "angstroms^2/fs"; + angularVelocity.title = "AngularVelocity"; + angularVelocity.dataType = "Vector3d"; + angularVelocity.accumulator.reserve(nBins_); + for (int i = 0; i < nBins_; i++) + angularVelocity.accumulator.push_back( new VectorAccumulator() ); + data_[ANGULARVELOCITY] = angularVelocity; + outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY; + + OutputData density; + density.units = "g cm^-3"; + density.title = "Density"; + density.dataType = "RealType"; + density.accumulator.reserve(nBins_); + for (int i = 0; i < nBins_; i++) + density.accumulator.push_back( new Accumulator() ); + data_[DENSITY] = density; + outputMap_["DENSITY"] = DENSITY; + + if (hasOutputFields) { + parseOutputFileFormat(rnemdParams->getOutputFields()); + } else { + if (usePeriodicBoundaryConditions_) + outputMask_.set(Z); + else + outputMask_.set(R); + switch (rnemdFluxType_) { + case rnemdKE: + case rnemdRotKE: + case rnemdFullKE: + outputMask_.set(TEMPERATURE); + break; + case rnemdPx: + case rnemdPy: + outputMask_.set(VELOCITY); + break; + case rnemdPz: + case rnemdPvector: + outputMask_.set(VELOCITY); + outputMask_.set(DENSITY); + break; + case rnemdLx: + case rnemdLy: + case rnemdLz: + case rnemdLvector: + outputMask_.set(ANGULARVELOCITY); + break; + case rnemdKeLx: + case rnemdKeLy: + case rnemdKeLz: + case rnemdKeLvector: + outputMask_.set(TEMPERATURE); + outputMask_.set(ANGULARVELOCITY); + break; + case rnemdKePx: + case rnemdKePy: + outputMask_.set(TEMPERATURE); + outputMask_.set(VELOCITY); + break; + case rnemdKePvector: + outputMask_.set(TEMPERATURE); + outputMask_.set(VELOCITY); + outputMask_.set(DENSITY); + break; + default: + break; + } + } + + if (hasOutputFileName) { + rnemdFileName_ = rnemdParams->getOutputFileName(); + } else { + rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd"; + } + + exchangeTime_ = rnemdParams->getExchangeTime(); + + Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot(); + // total exchange sums are zeroed out at the beginning: + + kineticExchange_ = 0.0; + momentumExchange_ = V3Zero; + angularMomentumExchange_ = V3Zero; + + std::ostringstream selectionAstream; + std::ostringstream selectionBstream; + + if (hasSelectionA_) { + selectionA_ = rnemdParams->getSelectionA(); + } else { + if (usePeriodicBoundaryConditions_) { + Mat3x3d hmat = currentSnap_->getHmat(); + + if (hasSlabWidth) + slabWidth_ = rnemdParams->getSlabWidth(); + else + slabWidth_ = hmat(2,2) / 10.0; + + if (hasSlabACenter) + slabACenter_ = rnemdParams->getSlabACenter(); + else + slabACenter_ = 0.0; + + selectionAstream << "select wrappedz > " + << slabACenter_ - 0.5*slabWidth_ + << " && wrappedz < " + << slabACenter_ + 0.5*slabWidth_; + selectionA_ = selectionAstream.str(); + } else { + if (hasSphereARadius) + sphereARadius_ = rnemdParams->getSphereARadius(); + else { + // use an initial guess to the size of the inner slab to be 1/10 the + // radius of an approximately spherical hull: + Thermo thermo(info); + RealType hVol = thermo.getHullVolume(); + sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0); + } + selectionAstream << "select r < " << sphereARadius_; + selectionA_ = selectionAstream.str(); + } + } + + if (hasSelectionB_) { + selectionB_ = rnemdParams->getSelectionB(); + } else { + if (usePeriodicBoundaryConditions_) { + Mat3x3d hmat = currentSnap_->getHmat(); + + if (hasSlabWidth) + slabWidth_ = rnemdParams->getSlabWidth(); + else + slabWidth_ = hmat(2,2) / 10.0; + + if (hasSlabBCenter) + slabBCenter_ = rnemdParams->getSlabBCenter(); + else + slabBCenter_ = hmat(2,2) / 2.0; + + selectionBstream << "select wrappedz > " + << slabBCenter_ - 0.5*slabWidth_ + << " && wrappedz < " + << slabBCenter_ + 0.5*slabWidth_; + selectionB_ = selectionBstream.str(); + } else { + if (hasSphereBRadius_) { + sphereBRadius_ = rnemdParams->getSphereBRadius(); + selectionBstream << "select r > " << sphereBRadius_; + selectionB_ = selectionBstream.str(); + } else { + selectionB_ = "select hull"; + hasSelectionB_ = true; + } + } + } + } + + // object evaluator: + evaluator_.loadScriptString(rnemdObjectSelection_); + seleMan_.setSelectionSet(evaluator_.evaluate()); + evaluatorA_.loadScriptString(selectionA_); + evaluatorB_.loadScriptString(selectionB_); + seleManA_.setSelectionSet(evaluatorA_.evaluate()); + seleManB_.setSelectionSet(evaluatorB_.evaluate()); + commonA_ = seleManA_ & seleMan_; + commonB_ = seleManB_ & seleMan_; } - RNEMD::~RNEMD() { - delete randNumGen_; + RNEMD::~RNEMD() { + if (!doRNEMD_) return; #ifdef IS_MPI if (worldRank == 0) { #endif - - sprintf(painCave.errMsg, - "RNEMD: total failed trials: %d\n", - failTrialCount_); - painCave.isFatal = 0; - painCave.severity = OPENMD_INFO; - simError(); - if (outputTemp_) tempLog_.close(); - if (outputVx_) vxzLog_.close(); - if (outputVy_) vyzLog_.close(); + writeOutputFile(); - if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || - rnemdType_ == rnemdPyScale) { - sprintf(painCave.errMsg, - "RNEMD: total root-checking warnings: %d\n", - failRootCount_); - painCave.isFatal = 0; - painCave.severity = OPENMD_INFO; - simError(); - } - if (output3DTemp_) { - xTempLog_.close(); - yTempLog_.close(); - zTempLog_.close(); - } - if (outputRotTemp_) rotTempLog_.close(); - + rnemdFile_.close(); + #ifdef IS_MPI } #endif + + // delete all of the objects we created: + delete areaAccumulator_; + data_.clear(); } + + void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) { + if (!doRNEMD_) return; + int selei; + int selej; - void RNEMD::doSwap() { - Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); - seleMan_.setSelectionSet(evaluator_.evaluate()); - - int selei; StuntDouble* sd; - int idx; RealType min_val; bool min_found = false; @@ -342,102 +628,132 @@ namespace OpenMD { bool max_found = false; StuntDouble* max_sd; - for (sd = seleMan_.beginSelected(selei); sd != NULL; - sd = seleMan_.nextSelected(selei)) { + for (sd = seleManA_.beginSelected(selei); sd != NULL; + sd = seleManA_.nextSelected(selei)) { - idx = sd->getLocalIndex(); - Vector3d pos = sd->getPos(); - + // wrap the stuntdouble's position back into the box: - + if (usePeriodicBoundaryConditions_) currentSnap_->wrapVector(pos); - - // which bin is this stuntdouble in? - // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] - - int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; - - - // if we're in bin 0 or the middleBin - if (binNo == 0 || binNo == midBin_) { + + RealType mass = sd->getMass(); + Vector3d vel = sd->getVel(); + RealType value; + + switch(rnemdFluxType_) { + case rnemdKE : - RealType mass = sd->getMass(); - Vector3d vel = sd->getVel(); - RealType value; - - switch(rnemdType_) { - case rnemdKineticSwap : + value = mass * vel.lengthSquare(); + + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); - value = mass * vel.lengthSquare(); - - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - value += angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - } else { - value += angMom[0]*angMom[0]/I(0, 0) - + angMom[1]*angMom[1]/I(1, 1) - + angMom[2]*angMom[2]/I(2, 2); - } - } //angular momenta exchange enabled - //energyConvert temporarily disabled - //make exchangeSum_ comparable between swap & scale - //value = value * 0.5 / PhysicalConstants::energyConvert; - value *= 0.5; - break; - case rnemdPx : - value = mass * vel[0]; - break; - case rnemdPy : - value = mass * vel[1]; - break; - case rnemdPz : - value = mass * vel[2]; - break; - default : - break; + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + value += angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k); + } else { + value += angMom[0]*angMom[0]/I(0, 0) + + angMom[1]*angMom[1]/I(1, 1) + + angMom[2]*angMom[2]/I(2, 2); + } + } //angular momenta exchange enabled + value *= 0.5; + break; + case rnemdPx : + value = mass * vel[0]; + break; + case rnemdPy : + value = mass * vel[1]; + break; + case rnemdPz : + value = mass * vel[2]; + break; + default : + break; + } + if (!max_found) { + max_val = value; + max_sd = sd; + max_found = true; + } else { + if (max_val < value) { + max_val = value; + max_sd = sd; } + } + } - if (binNo == 0) { - if (!min_found) { - min_val = value; - min_sd = sd; - min_found = true; - } else { - if (min_val > value) { - min_val = value; - min_sd = sd; - } - } - } else { //midBin_ - if (!max_found) { - max_val = value; - max_sd = sd; - max_found = true; - } else { - if (max_val < value) { - max_val = value; - max_sd = sd; - } - } - } + for (sd = seleManB_.beginSelected(selej); sd != NULL; + sd = seleManB_.nextSelected(selej)) { + + Vector3d pos = sd->getPos(); + + // wrap the stuntdouble's position back into the box: + + if (usePeriodicBoundaryConditions_) + currentSnap_->wrapVector(pos); + + RealType mass = sd->getMass(); + Vector3d vel = sd->getVel(); + RealType value; + + switch(rnemdFluxType_) { + case rnemdKE : + + value = mass * vel.lengthSquare(); + + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); + + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + value += angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k); + } else { + value += angMom[0]*angMom[0]/I(0, 0) + + angMom[1]*angMom[1]/I(1, 1) + + angMom[2]*angMom[2]/I(2, 2); + } + } //angular momenta exchange enabled + value *= 0.5; + break; + case rnemdPx : + value = mass * vel[0]; + break; + case rnemdPy : + value = mass * vel[1]; + break; + case rnemdPz : + value = mass * vel[2]; + break; + default : + break; } + + if (!min_found) { + min_val = value; + min_sd = sd; + min_found = true; + } else { + if (min_val > value) { + min_val = value; + min_sd = sd; + } + } } - -#ifdef IS_MPI - int nProc, worldRank; - - nProc = MPI::COMM_WORLD.Get_size(); - worldRank = MPI::COMM_WORLD.Get_rank(); - + +#ifdef IS_MPI + int worldRank = MPI::COMM_WORLD.Get_rank(); + bool my_min_found = min_found; bool my_max_found = max_found; @@ -454,7 +770,7 @@ namespace OpenMD { RealType val; int rank; } max_vals, min_vals; - + if (my_min_found) { min_vals.val = min_val; } else { @@ -492,8 +808,8 @@ namespace OpenMD { Vector3d max_vel = max_sd->getVel(); RealType temp_vel; - switch(rnemdType_) { - case rnemdKineticSwap : + switch(rnemdFluxType_) { + case rnemdKE : min_sd->setVel(max_vel); max_sd->setVel(min_vel); if (min_sd->isDirectional() && max_sd->isDirectional()) { @@ -544,8 +860,8 @@ namespace OpenMD { min_vel.getArrayPointer(), 3, MPI::REALTYPE, min_vals.rank, 0, status); - switch(rnemdType_) { - case rnemdKineticSwap : + switch(rnemdFluxType_) { + case rnemdKE : max_sd->setVel(min_vel); //angular momenta exchange enabled if (max_sd->isDirectional()) { @@ -590,8 +906,8 @@ namespace OpenMD { max_vel.getArrayPointer(), 3, MPI::REALTYPE, max_vals.rank, 0, status); - switch(rnemdType_) { - case rnemdKineticSwap : + switch(rnemdFluxType_) { + case rnemdKE : min_sd->setVel(max_vel); //angular momenta exchange enabled if (min_sd->isDirectional()) { @@ -625,10 +941,26 @@ namespace OpenMD { } } #endif - exchangeSum_ += max_val - min_val; + + switch(rnemdFluxType_) { + case rnemdKE: + kineticExchange_ += max_val - min_val; + break; + case rnemdPx: + momentumExchange_.x() += max_val - min_val; + break; + case rnemdPy: + momentumExchange_.y() += max_val - min_val; + break; + case rnemdPz: + momentumExchange_.z() += max_val - min_val; + break; + default: + break; + } } else { sprintf(painCave.errMsg, - "RNEMD: exchange NOT performed because min_val > max_val\n"); + "RNEMD::doSwap exchange NOT performed because min_val > max_val\n"); painCave.isFatal = 0; painCave.severity = OPENMD_INFO; simError(); @@ -636,26 +968,25 @@ namespace OpenMD { } } else { sprintf(painCave.errMsg, - "RNEMD: exchange NOT performed because selected object\n" - "\tnot present in at least one of the two slabs.\n"); + "RNEMD::doSwap exchange NOT performed because selected object\n" + "\twas not present in at least one of the two slabs.\n"); painCave.isFatal = 0; painCave.severity = OPENMD_INFO; simError(); failTrialCount_++; - } - + } } - void RNEMD::doScale() { + void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) { + if (!doRNEMD_) return; + int selei; + int selej; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); + RealType time = currentSnap_->getTime(); Mat3x3d hmat = currentSnap_->getHmat(); - seleMan_.setSelectionSet(evaluator_.evaluate()); - - int selei; StuntDouble* sd; - int idx; vector hotBin, coldBin; @@ -674,80 +1005,76 @@ namespace OpenMD { RealType Kcz = 0.0; RealType Kcw = 0.0; - for (sd = seleMan_.beginSelected(selei); sd != NULL; - sd = seleMan_.nextSelected(selei)) { + for (sd = smanA.beginSelected(selei); sd != NULL; + sd = smanA.nextSelected(selei)) { - idx = sd->getLocalIndex(); - Vector3d pos = sd->getPos(); - + // wrap the stuntdouble's position back into the box: - + if (usePeriodicBoundaryConditions_) currentSnap_->wrapVector(pos); - - // which bin is this stuntdouble in? - // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] - - int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; - - // if we're in bin 0 or the middleBin - if (binNo == 0 || binNo == midBin_) { - - RealType mass = sd->getMass(); - Vector3d vel = sd->getVel(); - - if (binNo == 0) { - hotBin.push_back(sd); - Phx += mass * vel.x(); - Phy += mass * vel.y(); - Phz += mass * vel.z(); - Khx += mass * vel.x() * vel.x(); - Khy += mass * vel.y() * vel.y(); - Khz += mass * vel.z() * vel.z(); - //if (rnemdType_ == rnemdKineticScaleVAM) { - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - Khw += angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - } else { - Khw += angMom[0]*angMom[0]/I(0, 0) - + angMom[1]*angMom[1]/I(1, 1) - + angMom[2]*angMom[2]/I(2, 2); - } - } - //} - } else { //midBin_ - coldBin.push_back(sd); - Pcx += mass * vel.x(); - Pcy += mass * vel.y(); - Pcz += mass * vel.z(); - Kcx += mass * vel.x() * vel.x(); - Kcy += mass * vel.y() * vel.y(); - Kcz += mass * vel.z() * vel.z(); - //if (rnemdType_ == rnemdKineticScaleVAM) { - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - Kcw += angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - } else { - Kcw += angMom[0]*angMom[0]/I(0, 0) - + angMom[1]*angMom[1]/I(1, 1) - + angMom[2]*angMom[2]/I(2, 2); - } - } - //} - } + + + RealType mass = sd->getMass(); + Vector3d vel = sd->getVel(); + + hotBin.push_back(sd); + Phx += mass * vel.x(); + Phy += mass * vel.y(); + Phz += mass * vel.z(); + Khx += mass * vel.x() * vel.x(); + Khy += mass * vel.y() * vel.y(); + Khz += mass * vel.z() * vel.z(); + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + Khw += angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k); + } else { + Khw += angMom[0]*angMom[0]/I(0, 0) + + angMom[1]*angMom[1]/I(1, 1) + + angMom[2]*angMom[2]/I(2, 2); + } + } + } + for (sd = smanB.beginSelected(selej); sd != NULL; + sd = smanB.nextSelected(selej)) { + Vector3d pos = sd->getPos(); + + // wrap the stuntdouble's position back into the box: + + if (usePeriodicBoundaryConditions_) + currentSnap_->wrapVector(pos); + + RealType mass = sd->getMass(); + Vector3d vel = sd->getVel(); + + coldBin.push_back(sd); + Pcx += mass * vel.x(); + Pcy += mass * vel.y(); + Pcz += mass * vel.z(); + Kcx += mass * vel.x() * vel.x(); + Kcy += mass * vel.y() * vel.y(); + Kcz += mass * vel.z() * vel.z(); + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + Kcw += angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k); + } else { + Kcw += angMom[0]*angMom[0]/I(0, 0) + + angMom[1]*angMom[1]/I(1, 1) + + angMom[2]*angMom[2]/I(2, 2); + } } } @@ -760,12 +1087,6 @@ namespace OpenMD { Kcz *= 0.5; Kcw *= 0.5; - std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz - << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy - << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n"; - std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz - << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " < 0 - if (rnemdType_ == rnemdKineticScaleVAM) { - c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw); + if (rnemdFluxType_ == rnemdFullKE) { + c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw); } else { - c = 1.0 - targetFlux_ / Kcw; + c = 1.0 - kineticTarget_ / Kcw; } if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients c = sqrt(c); - std::cerr << "cold slab scaling coefficient: " << c << endl; - //now convert to hotBin coefficient + RealType w = 0.0; - if (rnemdType_ == rnemdKineticScaleVAM) { + if (rnemdFluxType_ == rnemdFullKE) { x = 1.0 + px * (1.0 - c); y = 1.0 + py * (1.0 - c); z = 1.0 + pz * (1.0 - c); @@ -820,37 +1140,30 @@ namespace OpenMD { */ if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) && (fabs(z - 1.0) < 0.1)) { - w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y) + w = 1.0 + (kineticTarget_ + + Khx * (1.0 - x * x) + Khy * (1.0 - y * y) + Khz * (1.0 - z * z)) / Khw; }//no need to calculate w if x, y or z is out of range } else { - w = 1.0 + targetFlux_ / Khw; + w = 1.0 + kineticTarget_ / Khw; } if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients //if w is in the right range, so should be x, y, z. vector::iterator sdi; Vector3d vel; - for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { - if (rnemdType_ == rnemdKineticScaleVAM) { + for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) { + if (rnemdFluxType_ == rnemdFullKE) { vel = (*sdi)->getVel() * c; - //vel.x() *= c; - //vel.y() *= c; - //vel.z() *= c; (*sdi)->setVel(vel); } if ((*sdi)->isDirectional()) { Vector3d angMom = (*sdi)->getJ() * c; - //angMom[0] *= c; - //angMom[1] *= c; - //angMom[2] *= c; (*sdi)->setJ(angMom); } } w = sqrt(w); - std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z - << "\twh= " << w << endl; - for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { - if (rnemdType_ == rnemdKineticScaleVAM) { + for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) { + if (rnemdFluxType_ == rnemdFullKE) { vel = (*sdi)->getVel(); vel.x() *= x; vel.y() *= y; @@ -859,45 +1172,42 @@ namespace OpenMD { } if ((*sdi)->isDirectional()) { Vector3d angMom = (*sdi)->getJ() * w; - //angMom[0] *= w; - //angMom[1] *= w; - //angMom[2] *= w; (*sdi)->setJ(angMom); } } successfulScale = true; - exchangeSum_ += targetFlux_; + kineticExchange_ += kineticTarget_; } } } else { RealType a000, a110, c0, a001, a111, b01, b11, c1; - switch(rnemdType_) { - case rnemdKineticScale : + switch(rnemdFluxType_) { + case rnemdKE : /* used hotBin coeff's & only scale x & y dimensions RealType px = Phx / Pcx; RealType py = Phy / Pcy; a110 = Khy; - c0 = - Khx - Khy - targetFlux_; + c0 = - Khx - Khy - kineticTarget_; a000 = Khx; a111 = Kcy * py * py; b11 = -2.0 * Kcy * py * (1.0 + py); - c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_; + c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_; b01 = -2.0 * Kcx * px * (1.0 + px); a001 = Kcx * px * px; */ //scale all three dimensions, let c_x = c_y a000 = Kcx + Kcy; a110 = Kcz; - c0 = targetFlux_ - Kcx - Kcy - Kcz; + c0 = kineticTarget_ - Kcx - Kcy - Kcz; a001 = Khx * px * px + Khy * py * py; a111 = Khz * pz * pz; b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)); b11 = -2.0 * Khz * pz * (1.0 + pz); c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) - + Khz * pz * (2.0 + pz) - targetFlux_; + + Khz * pz * (2.0 + pz) - kineticTarget_; break; - case rnemdPxScale : - c = 1 - targetFlux_ / Pcx; + case rnemdPx : + c = 1 - momentumTarget_.x() / Pcx; a000 = Kcy; a110 = Kcz; c0 = Kcx * c * c - Kcx - Kcy - Kcz; @@ -908,8 +1218,8 @@ namespace OpenMD { c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) + Khx * (fastpow(c * px - px - 1.0, 2) - 1.0); break; - case rnemdPyScale : - c = 1 - targetFlux_ / Pcy; + case rnemdPy : + c = 1 - momentumTarget_.y() / Pcy; a000 = Kcx; a110 = Kcz; c0 = Kcy * c * c - Kcx - Kcy - Kcz; @@ -920,8 +1230,8 @@ namespace OpenMD { c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz) + Khy * (fastpow(c * py - py - 1.0, 2) - 1.0); break; - case rnemdPzScale ://we don't really do this, do we? - c = 1 - targetFlux_ / Pcz; + case rnemdPz ://we don't really do this, do we? + c = 1 - momentumTarget_.z() / Pcz; a000 = Kcx; a110 = Kcy; c0 = Kcz * c * c - Kcx - Kcy - Kcz; @@ -971,7 +1281,7 @@ namespace OpenMD { vector::iterator ri; RealType r1, r2, alpha0; vector > rps; - for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) { + for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) { r2 = *ri; //check if FindRealRoots() give the right answer if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { @@ -1003,24 +1313,24 @@ namespace OpenMD { RealType diff; pair bestPair = make_pair(1.0, 1.0); vector >::iterator rpi; - for (rpi = rps.begin(); rpi != rps.end(); rpi++) { + for (rpi = rps.begin(); rpi != rps.end(); ++rpi) { r1 = (*rpi).first; r2 = (*rpi).second; - switch(rnemdType_) { - case rnemdKineticScale : + switch(rnemdFluxType_) { + case rnemdKE : diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2) + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); break; - case rnemdPxScale : + case rnemdPx : diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); break; - case rnemdPyScale : + case rnemdPy : diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); break; - case rnemdPzScale : + case rnemdPz : diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); default : @@ -1034,33 +1344,33 @@ namespace OpenMD { #ifdef IS_MPI if (worldRank == 0) { #endif - sprintf(painCave.errMsg, - "RNEMD: roots r1= %lf\tr2 = %lf\n", - bestPair.first, bestPair.second); - painCave.isFatal = 0; - painCave.severity = OPENMD_INFO; - simError(); + // sprintf(painCave.errMsg, + // "RNEMD: roots r1= %lf\tr2 = %lf\n", + // bestPair.first, bestPair.second); + // painCave.isFatal = 0; + // painCave.severity = OPENMD_INFO; + // simError(); #ifdef IS_MPI } #endif - switch(rnemdType_) { - case rnemdKineticScale : + switch(rnemdFluxType_) { + case rnemdKE : x = bestPair.first; y = bestPair.first; z = bestPair.second; break; - case rnemdPxScale : + case rnemdPx : x = c; y = bestPair.first; z = bestPair.second; break; - case rnemdPyScale : + case rnemdPy : x = bestPair.first; y = c; z = bestPair.second; break; - case rnemdPzScale : + case rnemdPz : x = bestPair.first; y = bestPair.second; z = c; @@ -1070,7 +1380,7 @@ namespace OpenMD { } vector::iterator sdi; Vector3d vel; - for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { + for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) { vel = (*sdi)->getVel(); vel.x() *= x; vel.y() *= y; @@ -1081,7 +1391,7 @@ namespace OpenMD { x = 1.0 + px * (1.0 - x); y = 1.0 + py * (1.0 - y); z = 1.0 + pz * (1.0 - z); - for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { + for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) { vel = (*sdi)->getVel(); vel.x() *= x; vel.y() *= y; @@ -1089,167 +1399,299 @@ namespace OpenMD { (*sdi)->setVel(vel); } successfulScale = true; - exchangeSum_ += targetFlux_; + switch(rnemdFluxType_) { + case rnemdKE : + kineticExchange_ += kineticTarget_; + break; + case rnemdPx : + case rnemdPy : + case rnemdPz : + momentumExchange_ += momentumTarget_; + break; + default : + break; + } } } if (successfulScale != true) { sprintf(painCave.errMsg, - "RNEMD: exchange NOT performed!\n"); + "RNEMD::doNIVS exchange NOT performed - roots that solve\n" + "\tthe constraint equations may not exist or there may be\n" + "\tno selected objects in one or both slabs.\n"); painCave.isFatal = 0; painCave.severity = OPENMD_INFO; simError(); failTrialCount_++; } } + + void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) { + if (!doRNEMD_) return; + int selei; + int selej; - void RNEMD::doShiftScale() { - Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); + RealType time = currentSnap_->getTime(); Mat3x3d hmat = currentSnap_->getHmat(); - seleMan_.setSelectionSet(evaluator_.evaluate()); - - int selei; StuntDouble* sd; - int idx; vector hotBin, coldBin; Vector3d Ph(V3Zero); + Vector3d Lh(V3Zero); RealType Mh = 0.0; + Mat3x3d Ih(0.0); RealType Kh = 0.0; Vector3d Pc(V3Zero); + Vector3d Lc(V3Zero); RealType Mc = 0.0; + Mat3x3d Ic(0.0); RealType Kc = 0.0; - for (sd = seleMan_.beginSelected(selei); sd != NULL; - sd = seleMan_.nextSelected(selei)) { + // Constraints can be on only the linear or angular momentum, but + // not both. Usually, the user will specify which they want, but + // in case they don't, the use of periodic boundaries should make + // the choice for us. + bool doLinearPart = false; + bool doAngularPart = false; - idx = sd->getLocalIndex(); + switch (rnemdFluxType_) { + case rnemdPx: + case rnemdPy: + case rnemdPz: + case rnemdPvector: + case rnemdKePx: + case rnemdKePy: + case rnemdKePvector: + doLinearPart = true; + break; + case rnemdLx: + case rnemdLy: + case rnemdLz: + case rnemdLvector: + case rnemdKeLx: + case rnemdKeLy: + case rnemdKeLz: + case rnemdKeLvector: + doAngularPart = true; + break; + case rnemdKE: + case rnemdRotKE: + case rnemdFullKE: + default: + if (usePeriodicBoundaryConditions_) + doLinearPart = true; + else + doAngularPart = true; + break; + } + + for (sd = smanA.beginSelected(selei); sd != NULL; + sd = smanA.nextSelected(selei)) { Vector3d pos = sd->getPos(); // wrap the stuntdouble's position back into the box: + + if (usePeriodicBoundaryConditions_) + currentSnap_->wrapVector(pos); + + RealType mass = sd->getMass(); + Vector3d vel = sd->getVel(); + Vector3d rPos = sd->getPos() - coordinateOrigin_; + RealType r2; + + hotBin.push_back(sd); + Ph += mass * vel; + Mh += mass; + Kh += mass * vel.lengthSquare(); + Lh += mass * cross(rPos, vel); + Ih -= outProduct(rPos, rPos) * mass; + r2 = rPos.lengthSquare(); + Ih(0, 0) += mass * r2; + Ih(1, 1) += mass * r2; + Ih(2, 2) += mass * r2; + + if (rnemdFluxType_ == rnemdFullKE) { + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + Kh += angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k); + } else { + Kh += angMom[0] * angMom[0] / I(0, 0) + + angMom[1] * angMom[1] / I(1, 1) + + angMom[2] * angMom[2] / I(2, 2); + } + } + } + } + for (sd = smanB.beginSelected(selej); sd != NULL; + sd = smanB.nextSelected(selej)) { + Vector3d pos = sd->getPos(); + + // wrap the stuntdouble's position back into the box: + if (usePeriodicBoundaryConditions_) currentSnap_->wrapVector(pos); + + RealType mass = sd->getMass(); + Vector3d vel = sd->getVel(); + Vector3d rPos = sd->getPos() - coordinateOrigin_; + RealType r2; - // which bin is this stuntdouble in? - // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] - - int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; - - // if we're in bin 0 or the middleBin - if (binNo == 0 || binNo == midBin_) { - - RealType mass = sd->getMass(); - Vector3d vel = sd->getVel(); - - if (binNo == 0) { - hotBin.push_back(sd); - //std::cerr << "before, velocity = " << vel << endl; - Ph += mass * vel; - //std::cerr << "after, velocity = " << vel << endl; - Mh += mass; - Kh += mass * vel.lengthSquare(); - if (rnemdType_ == rnemdShiftScaleVAM) { - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - Kh += angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - } else { - Kh += angMom[0] * angMom[0] / I(0, 0) + - angMom[1] * angMom[1] / I(1, 1) + - angMom[2] * angMom[2] / I(2, 2); - } - } - } - } else { //midBin_ - coldBin.push_back(sd); - Pc += mass * vel; - Mc += mass; - Kc += mass * vel.lengthSquare(); - if (rnemdType_ == rnemdShiftScaleVAM) { - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - Kc += angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - } else { - Kc += angMom[0] * angMom[0] / I(0, 0) + - angMom[1] * angMom[1] / I(1, 1) + - angMom[2] * angMom[2] / I(2, 2); - } - } - } - } + coldBin.push_back(sd); + Pc += mass * vel; + Mc += mass; + Kc += mass * vel.lengthSquare(); + Lc += mass * cross(rPos, vel); + Ic -= outProduct(rPos, rPos) * mass; + r2 = rPos.lengthSquare(); + Ic(0, 0) += mass * r2; + Ic(1, 1) += mass * r2; + Ic(2, 2) += mass * r2; + + if (rnemdFluxType_ == rnemdFullKE) { + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + Kc += angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k); + } else { + Kc += angMom[0] * angMom[0] / I(0, 0) + + angMom[1] * angMom[1] / I(1, 1) + + angMom[2] * angMom[2] / I(2, 2); + } + } } } Kh *= 0.5; Kc *= 0.5; - - std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc - << "\tKc= " << Kc << endl; - std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl; - + #ifdef IS_MPI MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM); MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM); MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM); MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM); MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM); MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9, + MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9, + MPI::REALTYPE, MPI::SUM); #endif + + Vector3d ac, acrec, bc, bcrec; + Vector3d ah, ahrec, bh, bhrec; + bool successfulExchange = false; if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty Vector3d vc = Pc / Mc; - Vector3d ac = njzp_ / Mc + vc; - RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare(); + ac = -momentumTarget_ / Mc + vc; + acrec = -momentumTarget_ / Mc; + + // We now need the inverse of the inertia tensor to calculate the + // angular velocity of the cold slab; + Mat3x3d Ici = Ic.inverse(); + Vector3d omegac = Ici * Lc; + bc = -(Ici * angularMomentumTarget_) + omegac; + bcrec = bc - omegac; + + RealType cNumerator = Kc - kineticTarget_; + if (doLinearPart) + cNumerator -= 0.5 * Mc * ac.lengthSquare(); + + if (doAngularPart) + cNumerator -= 0.5 * ( dot(bc, Ic * bc)); + if (cNumerator > 0.0) { - RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare(); + + RealType cDenominator = Kc; + + if (doLinearPart) + cDenominator -= 0.5 * Mc * vc.lengthSquare(); + + if (doAngularPart) + cDenominator -= 0.5*(dot(omegac, Ic * omegac)); + if (cDenominator > 0.0) { RealType c = sqrt(cNumerator / cDenominator); if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients + Vector3d vh = Ph / Mh; - Vector3d ah = jzp_ / Mh + vh; - RealType hNumerator = Kh + targetJzKE_ - - 0.5 * Mh * ah.lengthSquare(); - if (hNumerator > 0.0) { - RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare(); + ah = momentumTarget_ / Mh + vh; + ahrec = momentumTarget_ / Mh; + + // We now need the inverse of the inertia tensor to + // calculate the angular velocity of the hot slab; + Mat3x3d Ihi = Ih.inverse(); + Vector3d omegah = Ihi * Lh; + bh = (Ihi * angularMomentumTarget_) + omegah; + bhrec = bh - omegah; + + RealType hNumerator = Kh + kineticTarget_; + if (doLinearPart) + hNumerator -= 0.5 * Mh * ah.lengthSquare(); + + if (doAngularPart) + hNumerator -= 0.5 * ( dot(bh, Ih * bh)); + + if (hNumerator > 0.0) { + + RealType hDenominator = Kh; + if (doLinearPart) + hDenominator -= 0.5 * Mh * vh.lengthSquare(); + if (doAngularPart) + hDenominator -= 0.5*(dot(omegah, Ih * omegah)); + if (hDenominator > 0.0) { RealType h = sqrt(hNumerator / hDenominator); if ((h > 0.9) && (h < 1.1)) { - std::cerr << "cold slab scaling coefficient: " << c << "\n"; - std::cerr << "hot slab scaling coefficient: " << h << "\n"; + vector::iterator sdi; Vector3d vel; - for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { + Vector3d rPos; + + for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) { //vel = (*sdi)->getVel(); - vel = ((*sdi)->getVel() - vc) * c + ac; + rPos = (*sdi)->getPos() - coordinateOrigin_; + if (doLinearPart) + vel = ((*sdi)->getVel() - vc) * c + ac; + if (doAngularPart) + vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos); + (*sdi)->setVel(vel); - if (rnemdType_ == rnemdShiftScaleVAM) { + if (rnemdFluxType_ == rnemdFullKE) { if ((*sdi)->isDirectional()) { Vector3d angMom = (*sdi)->getJ() * c; (*sdi)->setJ(angMom); } } } - for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { + for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) { //vel = (*sdi)->getVel(); - vel = ((*sdi)->getVel() - vh) * h + ah; + rPos = (*sdi)->getPos() - coordinateOrigin_; + if (doLinearPart) + vel = ((*sdi)->getVel() - vh) * h + ah; + if (doAngularPart) + vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos); + (*sdi)->setVel(vel); - if (rnemdType_ == rnemdShiftScaleVAM) { + if (rnemdFluxType_ == rnemdFullKE) { if ((*sdi)->isDirectional()) { Vector3d angMom = (*sdi)->getJ() * h; (*sdi)->setJ(angMom); @@ -1257,10 +1699,9 @@ namespace OpenMD { } } successfulExchange = true; - exchangeSum_ += targetFlux_; - // this is a redundant variable for doShiftScale() so that - // RNEMD can output one exchange quantity needed in a job. - // need a better way to do this. + kineticExchange_ += kineticTarget_; + momentumExchange_ += momentumTarget_; + angularMomentumExchange_ += angularMomentumTarget_; } } } @@ -1270,7 +1711,9 @@ namespace OpenMD { } if (successfulExchange != true) { sprintf(painCave.errMsg, - "RNEMD: exchange NOT performed!\n"); + "RNEMD::doVSS exchange NOT performed - roots that solve\n" + "\tthe constraint equations may not exist or there may be\n" + "\tno selected objects in one or both slabs.\n"); painCave.isFatal = 0; painCave.severity = OPENMD_INFO; simError(); @@ -1278,314 +1721,608 @@ namespace OpenMD { } } + RealType RNEMD::getDividingArea() { + + if (hasDividingArea_) return dividingArea_; + + RealType areaA, areaB; + Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); + + if (hasSelectionA_) { + int isd; + StuntDouble* sd; + vector aSites; + seleManA_.setSelectionSet(evaluatorA_.evaluate()); + for (sd = seleManA_.beginSelected(isd); sd != NULL; + sd = seleManA_.nextSelected(isd)) { + aSites.push_back(sd); + } +#if defined(HAVE_QHULL) + ConvexHull* surfaceMeshA = new ConvexHull(); + surfaceMeshA->computeHull(aSites); + areaA = surfaceMeshA->getArea(); + delete surfaceMeshA; +#else + sprintf( painCave.errMsg, + "RNEMD::getDividingArea : Hull calculation is not possible\n" + "\twithout libqhull. Please rebuild OpenMD with qhull enabled."); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); +#endif + + } else { + if (usePeriodicBoundaryConditions_) { + // in periodic boundaries, the surface area is twice the x-y + // area of the current box: + areaA = 2.0 * snap->getXYarea(); + } else { + // in non-periodic simulations, without explicitly setting + // selections, the sphere radius sets the surface area of the + // dividing surface: + areaA = 4.0 * M_PI * pow(sphereARadius_, 2); + } + } + + if (hasSelectionB_) { + int isd; + StuntDouble* sd; + vector bSites; + seleManB_.setSelectionSet(evaluatorB_.evaluate()); + for (sd = seleManB_.beginSelected(isd); sd != NULL; + sd = seleManB_.nextSelected(isd)) { + bSites.push_back(sd); + } + +#if defined(HAVE_QHULL) + ConvexHull* surfaceMeshB = new ConvexHull(); + surfaceMeshB->computeHull(bSites); + areaB = surfaceMeshB->getArea(); + delete surfaceMeshB; +#else + sprintf( painCave.errMsg, + "RNEMD::getDividingArea : Hull calculation is not possible\n" + "\twithout libqhull. Please rebuild OpenMD with qhull enabled."); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); +#endif + + + } else { + if (usePeriodicBoundaryConditions_) { + // in periodic boundaries, the surface area is twice the x-y + // area of the current box: + areaB = 2.0 * snap->getXYarea(); + } else { + // in non-periodic simulations, without explicitly setting + // selections, but if a sphereBradius has been set, just use that: + areaB = 4.0 * M_PI * pow(sphereBRadius_, 2); + } + } + + dividingArea_ = min(areaA, areaB); + hasDividingArea_ = true; + return dividingArea_; + } + void RNEMD::doRNEMD() { + if (!doRNEMD_) return; + trialCount_++; - switch(rnemdType_) { - case rnemdKineticScale : - case rnemdKineticScaleVAM : - case rnemdKineticScaleAM : - case rnemdPxScale : - case rnemdPyScale : - case rnemdPzScale : - doScale(); + // object evaluator: + evaluator_.loadScriptString(rnemdObjectSelection_); + seleMan_.setSelectionSet(evaluator_.evaluate()); + + evaluatorA_.loadScriptString(selectionA_); + evaluatorB_.loadScriptString(selectionB_); + + seleManA_.setSelectionSet(evaluatorA_.evaluate()); + seleManB_.setSelectionSet(evaluatorB_.evaluate()); + + commonA_ = seleManA_ & seleMan_; + commonB_ = seleManB_ & seleMan_; + + // Target exchange quantities (in each exchange) = dividingArea * dt * flux + // dt = exchange time interval + // flux = target flux + // dividingArea = smallest dividing surface between the two regions + + hasDividingArea_ = false; + RealType area = getDividingArea(); + + kineticTarget_ = kineticFlux_ * exchangeTime_ * area; + momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area; + angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area; + + switch(rnemdMethod_) { + case rnemdSwap: + doSwap(commonA_, commonB_); break; - case rnemdKineticSwap : - case rnemdPx : - case rnemdPy : - case rnemdPz : - doSwap(); + case rnemdNIVS: + doNIVS(commonA_, commonB_); break; - case rnemdShiftScaleV : - case rnemdShiftScaleVAM : - doShiftScale(); + case rnemdVSS: + doVSS(commonA_, commonB_); break; - case rnemdUnknown : + case rnemdUnkownMethod: default : break; } } void RNEMD::collectData() { - + if (!doRNEMD_) return; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); + + // collectData can be called more frequently than the doRNEMD, so use the + // computed area from the last exchange time: + RealType area = getDividingArea(); + areaAccumulator_->add(area); Mat3x3d hmat = currentSnap_->getHmat(); - seleMan_.setSelectionSet(evaluator_.evaluate()); - int selei; + int selei(0); StuntDouble* sd; - int idx; + int binNo; + vector binMass(nBins_, 0.0); + vector binPx(nBins_, 0.0); + vector binPy(nBins_, 0.0); + vector binPz(nBins_, 0.0); + vector binOmegax(nBins_, 0.0); + vector binOmegay(nBins_, 0.0); + vector binOmegaz(nBins_, 0.0); + vector binKE(nBins_, 0.0); + vector binDOF(nBins_, 0); + vector binCount(nBins_, 0); + // alternative approach, track all molecules instead of only those // selected for scaling/swapping: /* - SimInfo::MoleculeIterator miter; - vector::iterator iiter; - Molecule* mol; - StuntDouble* integrableObject; - for (mol = info_->beginMolecule(miter); mol != NULL; - mol = info_->nextMolecule(miter)) - integrableObject is essentially sd - for (integrableObject = mol->beginIntegrableObject(iiter); - integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(iiter)) + SimInfo::MoleculeIterator miter; + vector::iterator iiter; + Molecule* mol; + StuntDouble* sd; + for (mol = info_->beginMolecule(miter); mol != NULL; + mol = info_->nextMolecule(miter)) + sd is essentially sd + for (sd = mol->beginIntegrableObject(iiter); + sd != NULL; + sd = mol->nextIntegrableObject(iiter)) */ + for (sd = seleMan_.beginSelected(selei); sd != NULL; - sd = seleMan_.nextSelected(selei)) { - - idx = sd->getLocalIndex(); - + sd = seleMan_.nextSelected(selei)) { + Vector3d pos = sd->getPos(); // wrap the stuntdouble's position back into the box: - if (usePeriodicBoundaryConditions_) + if (usePeriodicBoundaryConditions_) { currentSnap_->wrapVector(pos); - - // which bin is this stuntdouble in? - // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] - - int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) % - rnemdLogWidth_; - // no symmetrization allowed due to arbitary rnemdLogWidth_ - /* - if (rnemdLogWidth_ == midBin_ + 1) - if (binNo > midBin_) - binNo = nBins_ - binNo; - */ + // which bin is this stuntdouble in? + // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] + // Shift molecules by half a box to have bins start at 0 + // The modulo operator is used to wrap the case when we are + // beyond the end of the bins back to the beginning. + binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_; + } else { + Vector3d rPos = pos - coordinateOrigin_; + binNo = int(rPos.length() / binWidth_); + } + RealType mass = sd->getMass(); - mHist_[binNo] += mass; Vector3d vel = sd->getVel(); - RealType value; - //RealType xVal, yVal, zVal; - - if (outputTemp_) { - value = mass * vel.lengthSquare(); - tempCount_[binNo] += 3; - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - value += angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - tempCount_[binNo] +=2; - } else { - value += angMom[0] * angMom[0] / I(0, 0) + - angMom[1]*angMom[1]/I(1, 1) + - angMom[2]*angMom[2]/I(2, 2); - tempCount_[binNo] +=3; - } - } - value = value / PhysicalConstants::energyConvert - / PhysicalConstants::kb;//may move to getStatus() - tempHist_[binNo] += value; + Vector3d rPos = sd->getPos() - coordinateOrigin_; + Vector3d aVel = cross(rPos, vel); + + if (binNo >= 0 && binNo < nBins_) { + binCount[binNo]++; + binMass[binNo] += mass; + binPx[binNo] += mass*vel.x(); + binPy[binNo] += mass*vel.y(); + binPz[binNo] += mass*vel.z(); + binOmegax[binNo] += aVel.x(); + binOmegay[binNo] += aVel.y(); + binOmegaz[binNo] += aVel.z(); + binKE[binNo] += 0.5 * (mass * vel.lengthSquare()); + binDOF[binNo] += 3; + + if (sd->isDirectional()) { + Vector3d angMom = sd->getJ(); + Mat3x3d I = sd->getI(); + if (sd->isLinear()) { + int i = sd->linearAxis(); + int j = (i + 1) % 3; + int k = (i + 2) % 3; + binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) + + angMom[k] * angMom[k] / I(k, k)); + binDOF[binNo] += 2; + } else { + binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) + + angMom[1] * angMom[1] / I(1, 1) + + angMom[2] * angMom[2] / I(2, 2)); + binDOF[binNo] += 3; + } + } } - if (outputVx_) { - value = mass * vel[0]; - //vxzCount_[binNo]++; - pxzHist_[binNo] += value; - } - if (outputVy_) { - value = mass * vel[1]; - //vyzCount_[binNo]++; - pyzHist_[binNo] += value; - } + } + +#ifdef IS_MPI + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0], + nBins_, MPI::INT, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0], + nBins_, MPI::REALTYPE, MPI::SUM); + MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0], + nBins_, MPI::INT, MPI::SUM); +#endif - if (output3DTemp_) { - value = mass * vel.x() * vel.x(); - xTempHist_[binNo] += value; - value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert - / PhysicalConstants::kb; - yTempHist_[binNo] += value; - value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert - / PhysicalConstants::kb; - zTempHist_[binNo] += value; - xyzTempCount_[binNo]++; + Vector3d vel; + Vector3d aVel; + RealType den; + RealType temp; + RealType z; + RealType r; + for (int i = 0; i < nBins_; i++) { + if (usePeriodicBoundaryConditions_) { + z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2); + den = binMass[i] * nBins_ * PhysicalConstants::densityConvert + / currentSnap_->getVolume() ; + } else { + r = (((RealType)i + 0.5) * binWidth_); + RealType rinner = (RealType)i * binWidth_; + RealType router = (RealType)(i+1) * binWidth_; + den = binMass[i] * 3.0 * PhysicalConstants::densityConvert + / (4.0 * M_PI * (pow(router,3) - pow(rinner,3))); } - if (outputRotTemp_) { - if (sd->isDirectional()) { - Vector3d angMom = sd->getJ(); - Mat3x3d I = sd->getI(); - if (sd->isLinear()) { - int i = sd->linearAxis(); - int j = (i + 1) % 3; - int k = (i + 2) % 3; - value = angMom[j] * angMom[j] / I(j, j) + - angMom[k] * angMom[k] / I(k, k); - rotTempCount_[binNo] +=2; - } else { - value = angMom[0] * angMom[0] / I(0, 0) + - angMom[1] * angMom[1] / I(1, 1) + - angMom[2] * angMom[2] / I(2, 2); - rotTempCount_[binNo] +=3; - } - } - value = value / PhysicalConstants::energyConvert - / PhysicalConstants::kb;//may move to getStatus() - rotTempHist_[binNo] += value; - } + vel.x() = binPx[i] / binMass[i]; + vel.y() = binPy[i] / binMass[i]; + vel.z() = binPz[i] / binMass[i]; + aVel.x() = binOmegax[i] / binCount[i]; + aVel.y() = binOmegay[i] / binCount[i]; + aVel.z() = binOmegaz[i] / binCount[i]; + if (binCount[i] > 0) { + // only add values if there are things to add + temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb * + PhysicalConstants::energyConvert); + + for (unsigned int j = 0; j < outputMask_.size(); ++j) { + if(outputMask_[j]) { + switch(j) { + case Z: + dynamic_cast(data_[j].accumulator[i])->add(z); + break; + case R: + dynamic_cast(data_[j].accumulator[i])->add(r); + break; + case TEMPERATURE: + dynamic_cast(data_[j].accumulator[i])->add(temp); + break; + case VELOCITY: + dynamic_cast(data_[j].accumulator[i])->add(vel); + break; + case ANGULARVELOCITY: + dynamic_cast(data_[j].accumulator[i])->add(aVel); + break; + case DENSITY: + dynamic_cast(data_[j].accumulator[i])->add(den); + break; + } + } + } + } } + hasData_ = true; } void RNEMD::getStarted() { + if (!doRNEMD_) return; + hasDividingArea_ = false; collectData(); - /*now can output profile in step 0, but might not be useful; - Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); - Stats& stat = currentSnap_->statData; - stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_; - */ - //may output a header for the log file here - getStatus(); + writeOutputFile(); } - void RNEMD::getStatus() { - - Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); - Stats& stat = currentSnap_->statData; - RealType time = currentSnap_->getTime(); - - stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_; - //or to be more meaningful, define another item as exchangeSum_ / time - int j; - + void RNEMD::parseOutputFileFormat(const std::string& format) { + if (!doRNEMD_) return; + StringTokenizer tokenizer(format, " ,;|\t\n\r"); + + while(tokenizer.hasMoreTokens()) { + std::string token(tokenizer.nextToken()); + toUpper(token); + OutputMapType::iterator i = outputMap_.find(token); + if (i != outputMap_.end()) { + outputMask_.set(i->second); + } else { + sprintf( painCave.errMsg, + "RNEMD::parseOutputFileFormat: %s is not a recognized\n" + "\toutputFileFormat keyword.\n", token.c_str() ); + painCave.isFatal = 0; + painCave.severity = OPENMD_ERROR; + simError(); + } + } + } + + void RNEMD::writeOutputFile() { + if (!doRNEMD_) return; + if (!hasData_) return; + #ifdef IS_MPI - - // all processors have the same number of bins, and STL vectors pack their - // arrays, so in theory, this should be safe: - - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - if (outputTemp_) { - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0], - rnemdLogWidth_, MPI::INT, MPI::SUM); - } - if (outputVx_) { - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - //MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0], - // rnemdLogWidth_, MPI::INT, MPI::SUM); - } - if (outputVy_) { - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - //MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0], - // rnemdLogWidth_, MPI::INT, MPI::SUM); - } - if (output3DTemp_) { - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0], - rnemdLogWidth_, MPI::INT, MPI::SUM); - } - if (outputRotTemp_) { - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0], - rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); - MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0], - rnemdLogWidth_, MPI::INT, MPI::SUM); - } - // If we're the root node, should we print out the results int worldRank = MPI::COMM_WORLD.Get_rank(); if (worldRank == 0) { #endif + rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc ); + + if( !rnemdFile_ ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for RNEMD output.\n", + rnemdFileName_.c_str()); + painCave.isFatal = 1; + simError(); + } - if (outputTemp_) { - tempLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j]; - } - tempLog_ << endl; + Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); + + RealType time = currentSnap_->getTime(); + RealType avgArea; + areaAccumulator_->getAverage(avgArea); + + RealType Jz(0.0); + Vector3d JzP(V3Zero); + Vector3d JzL(V3Zero); + if (time >= info_->getSimParams()->getDt()) { + Jz = kineticExchange_ / (time * avgArea) + / PhysicalConstants::energyConvert; + JzP = momentumExchange_ / (time * avgArea); + JzL = angularMomentumExchange_ / (time * avgArea); } - if (outputVx_) { - vxzLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - vxzLog_ << "\t" << pxzHist_[j] / mHist_[j]; - } - vxzLog_ << endl; + + rnemdFile_ << "#######################################################\n"; + rnemdFile_ << "# RNEMD {\n"; + + map::iterator mi; + for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) { + if ( (*mi).second == rnemdMethod_) + rnemdFile_ << "# exchangeMethod = \"" << (*mi).first << "\";\n"; } - if (outputVy_) { - vyzLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - vyzLog_ << "\t" << pyzHist_[j] / mHist_[j]; - } - vyzLog_ << endl; + map::iterator fi; + for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) { + if ( (*fi).second == rnemdFluxType_) + rnemdFile_ << "# fluxType = \"" << (*fi).first << "\";\n"; } + + rnemdFile_ << "# exchangeTime = " << exchangeTime_ << ";\n"; - if (output3DTemp_) { - RealType temp; - xTempLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - if (outputVx_) - xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j]; - temp = xTempHist_[j] / (RealType)xyzTempCount_[j] - / PhysicalConstants::energyConvert / PhysicalConstants::kb; - xTempLog_ << "\t" << temp; + rnemdFile_ << "# objectSelection = \"" + << rnemdObjectSelection_ << "\";\n"; + rnemdFile_ << "# selectionA = \"" << selectionA_ << "\";\n"; + rnemdFile_ << "# selectionB = \"" << selectionB_ << "\";\n"; + rnemdFile_ << "# }\n"; + rnemdFile_ << "#######################################################\n"; + rnemdFile_ << "# RNEMD report:\n"; + rnemdFile_ << "# running time = " << time << " fs\n"; + rnemdFile_ << "# Target flux:\n"; + rnemdFile_ << "# kinetic = " + << kineticFlux_ / PhysicalConstants::energyConvert + << " (kcal/mol/A^2/fs)\n"; + rnemdFile_ << "# momentum = " << momentumFluxVector_ + << " (amu/A/fs^2)\n"; + rnemdFile_ << "# angular momentum = " << angularMomentumFluxVector_ + << " (amu/A^2/fs^2)\n"; + rnemdFile_ << "# Target one-time exchanges:\n"; + rnemdFile_ << "# kinetic = " + << kineticTarget_ / PhysicalConstants::energyConvert + << " (kcal/mol)\n"; + rnemdFile_ << "# momentum = " << momentumTarget_ + << " (amu*A/fs)\n"; + rnemdFile_ << "# angular momentum = " << angularMomentumTarget_ + << " (amu*A^2/fs)\n"; + rnemdFile_ << "# Actual exchange totals:\n"; + rnemdFile_ << "# kinetic = " + << kineticExchange_ / PhysicalConstants::energyConvert + << " (kcal/mol)\n"; + rnemdFile_ << "# momentum = " << momentumExchange_ + << " (amu*A/fs)\n"; + rnemdFile_ << "# angular momentum = " << angularMomentumExchange_ + << " (amu*A^2/fs)\n"; + rnemdFile_ << "# Actual flux:\n"; + rnemdFile_ << "# kinetic = " << Jz + << " (kcal/mol/A^2/fs)\n"; + rnemdFile_ << "# momentum = " << JzP + << " (amu/A/fs^2)\n"; + rnemdFile_ << "# angular momentum = " << JzL + << " (amu/A^2/fs^2)\n"; + rnemdFile_ << "# Exchange statistics:\n"; + rnemdFile_ << "# attempted = " << trialCount_ << "\n"; + rnemdFile_ << "# failed = " << failTrialCount_ << "\n"; + if (rnemdMethod_ == rnemdNIVS) { + rnemdFile_ << "# NIVS root-check errors = " + << failRootCount_ << "\n"; + } + rnemdFile_ << "#######################################################\n"; + + + + //write title + rnemdFile_ << "#"; + for (unsigned int i = 0; i < outputMask_.size(); ++i) { + if (outputMask_[i]) { + rnemdFile_ << "\t" << data_[i].title << + "(" << data_[i].units << ")"; + // add some extra tabs for column alignment + if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t"; } - xTempLog_ << endl; - yTempLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j]; - } - yTempLog_ << endl; - zTempLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j]; - } - zTempLog_ << endl; } - if (outputRotTemp_) { - rotTempLog_ << time; - for (j = 0; j < rnemdLogWidth_; j++) { - rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j]; - } - rotTempLog_ << endl; - } + rnemdFile_ << std::endl; + + rnemdFile_.precision(8); + + for (int j = 0; j < nBins_; j++) { + + for (unsigned int i = 0; i < outputMask_.size(); ++i) { + if (outputMask_[i]) { + if (data_[i].dataType == "RealType") + writeReal(i,j); + else if (data_[i].dataType == "Vector3d") + writeVector(i,j); + else { + sprintf( painCave.errMsg, + "RNEMD found an unknown data type for: %s ", + data_[i].title.c_str()); + painCave.isFatal = 1; + simError(); + } + } + } + rnemdFile_ << std::endl; + + } + rnemdFile_ << "#######################################################\n"; + rnemdFile_ << "# Standard Deviations in those quantities follow:\n"; + rnemdFile_ << "#######################################################\n"; + + + for (int j = 0; j < nBins_; j++) { + rnemdFile_ << "#"; + for (unsigned int i = 0; i < outputMask_.size(); ++i) { + if (outputMask_[i]) { + if (data_[i].dataType == "RealType") + writeRealStdDev(i,j); + else if (data_[i].dataType == "Vector3d") + writeVectorStdDev(i,j); + else { + sprintf( painCave.errMsg, + "RNEMD found an unknown data type for: %s ", + data_[i].title.c_str()); + painCave.isFatal = 1; + simError(); + } + } + } + rnemdFile_ << std::endl; + + } + + rnemdFile_.flush(); + rnemdFile_.close(); + #ifdef IS_MPI } #endif + + } + + void RNEMD::writeReal(int index, unsigned int bin) { + if (!doRNEMD_) return; + assert(index >=0 && index < ENDINDEX); + assert(int(bin) < nBins_); + RealType s; + int count; + + count = data_[index].accumulator[bin]->count(); + if (count == 0) return; + + dynamic_cast(data_[index].accumulator[bin])->getAverage(s); + + if (! isinf(s) && ! isnan(s)) { + rnemdFile_ << "\t" << s; + } else{ + sprintf( painCave.errMsg, + "RNEMD detected a numerical error writing: %s for bin %u", + data_[index].title.c_str(), bin); + painCave.isFatal = 1; + simError(); + } + } + + void RNEMD::writeVector(int index, unsigned int bin) { + if (!doRNEMD_) return; + assert(index >=0 && index < ENDINDEX); + assert(int(bin) < nBins_); + Vector3d s; + int count; + + count = data_[index].accumulator[bin]->count(); - for (j = 0; j < rnemdLogWidth_; j++) { - mHist_[j] = 0.0; + if (count == 0) return; + + dynamic_cast(data_[index].accumulator[bin])->getAverage(s); + if (isinf(s[0]) || isnan(s[0]) || + isinf(s[1]) || isnan(s[1]) || + isinf(s[2]) || isnan(s[2]) ) { + sprintf( painCave.errMsg, + "RNEMD detected a numerical error writing: %s for bin %u", + data_[index].title.c_str(), bin); + painCave.isFatal = 1; + simError(); + } else { + rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; } - if (outputTemp_) - for (j = 0; j < rnemdLogWidth_; j++) { - tempCount_[j] = 0; - tempHist_[j] = 0.0; - } - if (outputVx_) - for (j = 0; j < rnemdLogWidth_; j++) { - //pxzCount_[j] = 0; - pxzHist_[j] = 0.0; - } - if (outputVy_) - for (j = 0; j < rnemdLogWidth_; j++) { - //pyzCount_[j] = 0; - pyzHist_[j] = 0.0; - } + } - if (output3DTemp_) - for (j = 0; j < rnemdLogWidth_; j++) { - xTempHist_[j] = 0.0; - yTempHist_[j] = 0.0; - zTempHist_[j] = 0.0; - xyzTempCount_[j] = 0; - } - if (outputRotTemp_) - for (j = 0; j < rnemdLogWidth_; j++) { - rotTempCount_[j] = 0; - rotTempHist_[j] = 0.0; - } + void RNEMD::writeRealStdDev(int index, unsigned int bin) { + if (!doRNEMD_) return; + assert(index >=0 && index < ENDINDEX); + assert(int(bin) < nBins_); + RealType s; + int count; + + count = data_[index].accumulator[bin]->count(); + if (count == 0) return; + + dynamic_cast(data_[index].accumulator[bin])->getStdDev(s); + + if (! isinf(s) && ! isnan(s)) { + rnemdFile_ << "\t" << s; + } else{ + sprintf( painCave.errMsg, + "RNEMD detected a numerical error writing: %s std. dev. for bin %u", + data_[index].title.c_str(), bin); + painCave.isFatal = 1; + simError(); + } } + + void RNEMD::writeVectorStdDev(int index, unsigned int bin) { + if (!doRNEMD_) return; + assert(index >=0 && index < ENDINDEX); + assert(int(bin) < nBins_); + Vector3d s; + int count; + + count = data_[index].accumulator[bin]->count(); + if (count == 0) return; + + dynamic_cast(data_[index].accumulator[bin])->getStdDev(s); + if (isinf(s[0]) || isnan(s[0]) || + isinf(s[1]) || isnan(s[1]) || + isinf(s[2]) || isnan(s[2]) ) { + sprintf( painCave.errMsg, + "RNEMD detected a numerical error writing: %s std. dev. for bin %u", + data_[index].title.c_str(), bin); + painCave.isFatal = 1; + simError(); + } else { + rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; + } + } }