--- trunk/src/rnemd/RNEMD.cpp 2012/10/17 19:04:44 1804 +++ trunk/src/rnemd/RNEMD.cpp 2013/06/16 15:15:42 1879 @@ -35,11 +35,14 @@ * * [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 +#include + #include "rnemd/RNEMD.hpp" #include "math/Vector3.hpp" #include "math/Vector.hpp" @@ -49,6 +52,8 @@ #include "primitives/StuntDouble.hpp" #include "utils/PhysicalConstants.hpp" #include "utils/Tuple.hpp" +#include "brains/Thermo.hpp" +#include "math/ConvexHull.hpp" #ifdef IS_MPI #include #endif @@ -64,13 +69,17 @@ namespace OpenMD { 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; - Globals * simParams = info->getSimParams(); + Globals* simParams = info->getSimParams(); RNEMDParameters* rnemdParams = simParams->getRNEMDParameters(); doRNEMD_ = rnemdParams->getUseRNEMD(); @@ -85,20 +94,26 @@ namespace OpenMD { 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; runTime_ = simParams->getRunTime(); statusTime_ = simParams->getStatusTime(); - rnemdObjectSelection_ = rnemdParams->getObjectSelection(); - evaluator_.loadScriptString(rnemdObjectSelection_); - seleMan_.setSelectionSet(evaluator_.evaluate()); - const string methStr = rnemdParams->getMethod(); bool hasFluxType = rnemdParams->haveFluxType(); + rnemdObjectSelection_ = rnemdParams->getObjectSelection(); + string fluxStr; if (hasFluxType) { fluxStr = rnemdParams->getFluxType(); @@ -106,7 +121,8 @@ namespace OpenMD { sprintf(painCave.errMsg, "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, KE+Px, KE+Py, KE+Pvector\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; @@ -116,9 +132,16 @@ namespace OpenMD { 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(); @@ -203,16 +226,32 @@ namespace OpenMD { 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; @@ -235,7 +274,8 @@ namespace OpenMD { 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, and momentumFluxVector\n", + "\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n" + "\tmomentumFluxVector, and angularMomentumFluxVector.\n", methStr.c_str(), fluxStr.c_str()); painCave.isFatal = 1; painCave.severity = OPENMD_ERROR; @@ -275,152 +315,282 @@ namespace OpenMD { default: break; } - } - } + } + 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; + } + } + } - // do some sanity checking + if (hasCoordinateOrigin) { + coordinateOrigin_ = rnemdParams->getCoordinateOrigin(); + } else { + coordinateOrigin_ = V3Zero; + } - int selectionCount = seleMan_.getSelectionCount(); + // do some sanity checking - int nIntegrable = info->getNGlobalIntegrableObjects(); + int selectionCount = seleMan_.getSelectionCount(); - 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(); - } + int nIntegrable = info->getNGlobalIntegrableObjects(); - areaAccumulator_ = new Accumulator(); + 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(); + } - nBins_ = rnemdParams->getOutputBins(); + areaAccumulator_ = new Accumulator(); - 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; + nBins_ = rnemdParams->getOutputBins(); + binWidth_ = rnemdParams->getOutputBinWidth(); - 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; + 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 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 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; + 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; - if (hasOutputFields) { - parseOutputFileFormat(rnemdParams->getOutputFields()); - } else { - outputMask_.set(Z); - 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 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"; - } + 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; - exchangeTime_ = rnemdParams->getExchangeTime(); + 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; - Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot(); - Mat3x3d hmat = currentSnap_->getHmat(); - - // Target exchange quantities (in each exchange) = 2 Lx Ly dt flux - // Lx, Ly = box dimensions in x & y - // dt = exchange time interval - // flux = target flux + 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; - RealType area = currentSnap_->getXYarea(); - kineticTarget_ = 2.0 * kineticFlux_ * exchangeTime_ * area; - momentumTarget_ = 2.0 * momentumFluxVector_ * exchangeTime_ * area; + 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; - // total exchange sums are zeroed out at the beginning: + 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"; + } - kineticExchange_ = 0.0; - momentumExchange_ = V3Zero; + exchangeTime_ = rnemdParams->getExchangeTime(); - if (hasSlabWidth) - slabWidth_ = rnemdParams->getSlabWidth(); - else - slabWidth_ = hmat(2,2) / 10.0; - - if (hasSlabACenter) - slabACenter_ = rnemdParams->getSlabACenter(); - else - slabACenter_ = 0.0; + 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 (hasSlabBCenter) - slabBCenter_ = rnemdParams->getSlabBCenter(); - else - slabBCenter_ = hmat(2,2) / 2.0; + 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() { if (!doRNEMD_) return; #ifdef IS_MPI @@ -434,23 +604,20 @@ namespace OpenMD { #ifdef IS_MPI } #endif + + // delete all of the objects we created: + delete areaAccumulator_; + data_.clear(); } - bool RNEMD::inSlabA(Vector3d pos) { - return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_); - } - bool RNEMD::inSlabB(Vector3d pos) { - return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_); - } - - void RNEMD::doSwap() { + void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) { if (!doRNEMD_) return; + int selei; + int selej; + Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); - seleMan_.setSelectionSet(evaluator_.evaluate()); - - int selei; StuntDouble* sd; RealType min_val; @@ -461,84 +628,127 @@ 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)) { Vector3d pos = sd->getPos(); - + // wrap the stuntdouble's position back into the box: - + if (usePeriodicBoundaryConditions_) currentSnap_->wrapVector(pos); - bool inA = inSlabA(pos); - bool inB = inSlabB(pos); - - if (inA || inB) { + + 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(rnemdFluxType_) { - case rnemdKE : + 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 - 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 (inA == 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 { - 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 @@ -767,14 +977,15 @@ namespace OpenMD { } } - void RNEMD::doNIVS() { + 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; vector hotBin, coldBin; @@ -794,72 +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)) { Vector3d pos = sd->getPos(); - + // wrap the stuntdouble's position back into the box: - + if (usePeriodicBoundaryConditions_) currentSnap_->wrapVector(pos); - - // which bin is this stuntdouble in? - bool inA = inSlabA(pos); - bool inB = inSlabB(pos); + + + 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(); - if (inA || inB) { - - RealType mass = sd->getMass(); - Vector3d vel = sd->getVel(); - - if (inA) { - 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); - } - } - } else { - 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); - } - } - } + 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); + } } } @@ -936,7 +1151,7 @@ namespace OpenMD { //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++) { + for (sdi = coldBin.begin(); sdi != coldBin.end(); ++sdi) { if (rnemdFluxType_ == rnemdFullKE) { vel = (*sdi)->getVel() * c; (*sdi)->setVel(vel); @@ -947,7 +1162,7 @@ namespace OpenMD { } } w = sqrt(w); - for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { + for (sdi = hotBin.begin(); sdi != hotBin.end(); ++sdi) { if (rnemdFluxType_ == rnemdFullKE) { vel = (*sdi)->getVel(); vel.x() *= x; @@ -1066,7 +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 ) { @@ -1098,7 +1313,7 @@ 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(rnemdFluxType_) { @@ -1165,7 +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; @@ -1176,7 +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; @@ -1209,92 +1424,155 @@ namespace OpenMD { failTrialCount_++; } } - - void RNEMD::doVSS() { + + void RNEMD::doVSS(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; 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; + 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? - bool inA = inSlabA(pos); - bool inB = inSlabB(pos); + 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 (inA || inB) { - - RealType mass = sd->getMass(); - Vector3d vel = sd->getVel(); - - if (inA) { - hotBin.push_back(sd); - Ph += mass * vel; - Mh += mass; - Kh += mass * vel.lengthSquare(); - 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); - } - } - } - } else { //midBin_ - coldBin.push_back(sd); - Pc += mass * vel; - Mc += mass; - Kc += mass * vel.lengthSquare(); - 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); - } - } - } - } + 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); + } + } } } @@ -1304,39 +1582,98 @@ namespace OpenMD { #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 = -momentumTarget_ / Mc + vc; - Vector3d acrec = -momentumTarget_ / Mc; - RealType cNumerator = Kc - kineticTarget_ - 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 = momentumTarget_ / Mh + vh; - Vector3d ahrec = momentumTarget_ / Mh; - RealType hNumerator = Kh + kineticTarget_ - - 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)) { - + 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 (rnemdFluxType_ == rnemdFullKE) { if ((*sdi)->isDirectional()) { @@ -1345,9 +1682,14 @@ namespace OpenMD { } } } - 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 (rnemdFluxType_ == rnemdFullKE) { if ((*sdi)->isDirectional()) { @@ -1359,6 +1701,7 @@ namespace OpenMD { successfulExchange = true; kineticExchange_ += kineticTarget_; momentumExchange_ += momentumTarget_; + angularMomentumExchange_ += angularMomentumTarget_; } } } @@ -1378,18 +1721,129 @@ 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_++; + + // 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(); + doSwap(commonA_, commonB_); break; case rnemdNIVS: - doNIVS(); + doNIVS(commonA_, commonB_); break; case rnemdVSS: - doVSS(); + doVSS(commonA_, commonB_); break; case rnemdUnkownMethod: default : @@ -1400,19 +1854,25 @@ namespace OpenMD { 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(); - - areaAccumulator_->add(currentSnap_->getXYarea()); - seleMan_.setSelectionSet(evaluator_.evaluate()); int selei(0); StuntDouble* sd; + 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); @@ -1420,16 +1880,16 @@ namespace OpenMD { // alternative approach, track all molecules instead of only those // selected for scaling/swapping: /* - SimInfo::MoleculeIterator miter; - vector::iterator iiter; - Molecule* mol; - StuntDouble* sd; - for (mol = info_->beginMolecule(miter); mol != NULL; + 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 = mol->beginIntegrableObject(iiter); + sd != NULL; + sd = mol->nextIntegrableObject(iiter)) */ for (sd = seleMan_.beginSelected(selei); sd != NULL; @@ -1439,43 +1899,52 @@ namespace OpenMD { // 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)] + // 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_); + } - - // 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. - int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_; - RealType mass = sd->getMass(); Vector3d vel = sd->getVel(); - - binCount[binNo]++; - binMass[binNo] += mass; - binPx[binNo] += mass*vel.x(); - binPy[binNo] += mass*vel.y(); - binPz[binNo] += mass*vel.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; + 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; + } } } } @@ -1491,6 +1960,12 @@ namespace OpenMD { 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], @@ -1498,18 +1973,30 @@ namespace OpenMD { #endif Vector3d vel; + Vector3d aVel; RealType den; RealType temp; RealType z; + RealType r; for (int i = 0; i < nBins_; i++) { - z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2); + 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))); + } 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]; - den = binMass[i] * nBins_ * PhysicalConstants::densityConvert - / currentSnap_->getVolume() ; - if (binCount[i] > 0) { // only add values if there are things to add temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb * @@ -1521,12 +2008,18 @@ namespace OpenMD { 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; @@ -1535,10 +2028,12 @@ namespace OpenMD { } } } + hasData_ = true; } void RNEMD::getStarted() { if (!doRNEMD_) return; + hasDividingArea_ = false; collectData(); writeOutputFile(); } @@ -1566,6 +2061,7 @@ namespace OpenMD { void RNEMD::writeOutputFile() { if (!doRNEMD_) return; + if (!hasData_) return; #ifdef IS_MPI // If we're the root node, should we print out the results @@ -1587,10 +2083,17 @@ namespace OpenMD { RealType time = currentSnap_->getTime(); RealType avgArea; areaAccumulator_->getAverage(avgArea); - RealType Jz = kineticExchange_ / (2.0 * time * avgArea) - / PhysicalConstants::energyConvert; - Vector3d JzP = momentumExchange_ / (2.0 * time * 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); + } + rnemdFile_ << "#######################################################\n"; rnemdFile_ << "# RNEMD {\n"; @@ -1609,41 +2112,48 @@ namespace OpenMD { rnemdFile_ << "# objectSelection = \"" << rnemdObjectSelection_ << "\";\n"; - rnemdFile_ << "# slabWidth = " << slabWidth_ << ";\n"; - rnemdFile_ << "# slabAcenter = " << slabACenter_ << ";\n"; - rnemdFile_ << "# slabBcenter = " << slabBCenter_ << ";\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 = " + rnemdFile_ << "# running time = " << time << " fs\n"; + rnemdFile_ << "# Target flux:\n"; + rnemdFile_ << "# kinetic = " << kineticFlux_ / PhysicalConstants::energyConvert << " (kcal/mol/A^2/fs)\n"; - rnemdFile_ << "# momentum = " << momentumFluxVector_ + rnemdFile_ << "# momentum = " << momentumFluxVector_ << " (amu/A/fs^2)\n"; - rnemdFile_ << "# target one-time exchanges:\n"; - rnemdFile_ << "# kinetic = " + 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_ + rnemdFile_ << "# momentum = " << momentumTarget_ << " (amu*A/fs)\n"; - rnemdFile_ << "# actual exchange totals:\n"; - rnemdFile_ << "# kinetic = " + 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_ + rnemdFile_ << "# momentum = " << momentumExchange_ << " (amu*A/fs)\n"; - rnemdFile_ << "# actual flux:\n"; - rnemdFile_ << "# kinetic = " << Jz + 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 + rnemdFile_ << "# momentum = " << JzP << " (amu/A/fs^2)\n"; - rnemdFile_ << "# exchange statistics:\n"; - rnemdFile_ << "# attempted = " << trialCount_ << "\n"; - rnemdFile_ << "# failed = " << failTrialCount_ << "\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 = " + rnemdFile_ << "# NIVS root-check errors = " << failRootCount_ << "\n"; } rnemdFile_ << "#######################################################\n"; @@ -1670,7 +2180,7 @@ namespace OpenMD { if (outputMask_[i]) { if (data_[i].dataType == "RealType") writeReal(i,j); - else if (data_[i].dataType == "Vector3d") + else if (data_[i].dataType == "Vector3d") writeVector(i,j); else { sprintf( painCave.errMsg, @@ -1723,16 +2233,20 @@ namespace OpenMD { void RNEMD::writeReal(int index, unsigned int bin) { if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); - assert(bin < nBins_); + 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 %d", + "RNEMD detected a numerical error writing: %s for bin %u", data_[index].title.c_str(), bin); painCave.isFatal = 1; simError(); @@ -1742,14 +2256,20 @@ namespace OpenMD { void RNEMD::writeVector(int index, unsigned int bin) { if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); - assert(bin < nBins_); + assert(int(bin) < nBins_); Vector3d s; + int count; + + count = data_[index].accumulator[bin]->count(); + + 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 %d", + "RNEMD detected a numerical error writing: %s for bin %u", data_[index].title.c_str(), bin); painCave.isFatal = 1; simError(); @@ -1761,16 +2281,20 @@ namespace OpenMD { void RNEMD::writeRealStdDev(int index, unsigned int bin) { if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); - assert(bin < nBins_); + 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 %d", + "RNEMD detected a numerical error writing: %s std. dev. for bin %u", data_[index].title.c_str(), bin); painCave.isFatal = 1; simError(); @@ -1780,14 +2304,19 @@ namespace OpenMD { void RNEMD::writeVectorStdDev(int index, unsigned int bin) { if (!doRNEMD_) return; assert(index >=0 && index < ENDINDEX); - assert(bin < nBins_); + 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 %d", + "RNEMD detected a numerical error writing: %s std. dev. for bin %u", data_[index].title.c_str(), bin); painCave.isFatal = 1; simError();