--- trunk/src/integrators/RNEMD.cpp 2009/04/23 18:31:05 1339 +++ branches/development/src/integrators/RNEMD.cpp 2012/05/24 20:59:54 1723 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,60 +28,245 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [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). + * [4] Vardeman & Gezelter, in progress (2009). */ +#include #include "integrators/RNEMD.hpp" #include "math/Vector3.hpp" +#include "math/Vector.hpp" #include "math/SquareMatrix3.hpp" +#include "math/Polynomial.hpp" #include "primitives/Molecule.hpp" #include "primitives/StuntDouble.hpp" -#include "utils/OOPSEConstant.hpp" +#include "utils/PhysicalConstants.hpp" #include "utils/Tuple.hpp" #ifndef IS_MPI #include "math/SeqRandNumGen.hpp" #else #include "math/ParallelRandNumGen.hpp" +#include #endif -/* Remove me after testing*/ -/* -#include -#include -*/ -/*End remove me*/ +#define HONKING_LARGE_VALUE 1.0e10 -namespace oopse { +using namespace std; +namespace OpenMD { - RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { - + RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), + usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { + + failTrialCount_ = 0; + failRootCount_ = 0; + int seedValue; Globals * simParams = info->getSimParams(); - stringToEnumMap_["Kinetic"] = rnemdKinetic; + 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; rnemdObjectSelection_ = simParams->getRNEMD_objectSelection(); - - std::cerr << "calling evaluator with " << rnemdObjectSelection_ << "\n"; evaluator_.loadScriptString(rnemdObjectSelection_); - std::cerr << "done\n"; + seleMan_.setSelectionSet(evaluator_.evaluate()); + + // do some sanity checking + + int selectionCount = seleMan_.getSelectionCount(); + int nIntegrable = info->getNGlobalIntegrableObjects(); + + if (selectionCount > nIntegrable) { + 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; + simError(); + } - const std::string st = simParams->getRNEMD_swapType(); + const string st = simParams->getRNEMD_exchangeType(); - std::map::iterator i; + map::iterator i; i = stringToEnumMap_.find(st); - rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second; + rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second; + if (rnemdType_ == rnemdUnknown) { + sprintf(painCave.errMsg, + "RNEMD: The current RNEMD_exchangeType,\n" + "\t\t%s\n" + "\tis not one of the recognized exchange types.\n", + st.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(); + } - set_RNEMD_swapTime(simParams->getRNEMD_swapTime()); +#ifdef IS_MPI + if (worldRank == 0) { +#endif + + //may have rnemdWriter separately + string rnemdFileName; + + if (outputTemp_) { + rnemdFileName = "temperature.log"; + tempLog_.open(rnemdFileName.c_str()); + } + if (outputVx_) { + rnemdFileName = "velocityX.log"; + vxzLog_.open(rnemdFileName.c_str()); + } + if (outputVy_) { + rnemdFileName = "velocityY.log"; + vyzLog_.open(rnemdFileName.c_str()); + } + + 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 (outputRotTemp_) { + rnemdFileName = "temperatureR.log"; + rotTempLog_.open(rnemdFileName.c_str()); + } + +#ifdef IS_MPI + } +#endif + + set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime()); set_RNEMD_nBins(simParams->getRNEMD_nBins()); - exchangeSum_ = 0.0; - counter_ = 0; //added by shenyu - //profile_.open("profile", std::ios::out); + midBin_ = nBins_ / 2; + if (simParams->haveRNEMD_binShift()) { + if (simParams->getRNEMD_binShift()) { + zShift_ = 0.5 / (RealType)(nBins_); + } else { + zShift_ = 0.0; + } + } 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); + 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_; + #ifndef IS_MPI if (simParams->haveSeed()) { seedValue = simParams->getSeed(); @@ -110,27 +286,50 @@ namespace oopse { RNEMD::~RNEMD() { delete randNumGen_; - //profile_.close(); + +#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(); + + 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(); + +#ifdef IS_MPI + } +#endif } void RNEMD::doSwap() { - //std::cerr << "in RNEMD!\n"; - //std::cerr << "nBins = " << nBins_ << "\n"; - int midBin = nBins_ / 2; - //std::cerr << "midBin = " << midBin << "\n"; - //std::cerr << "swapTime = " << swapTime_ << "\n"; - //std::cerr << "swapType = " << rnemdType_ << "\n"; - //std::cerr << "selection = " << rnemdObjectSelection_ << "\n"; Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); - //std::cerr << "hmat = " << hmat << "\n"; - seleMan_.setSelectionSet(evaluator_.evaluate()); - //std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n"; - int selei; StuntDouble* sd; int idx; @@ -158,40 +357,41 @@ namespace oopse { // 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_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2)); + int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; - //std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n"; // if we're in bin 0 or the middleBin - if (binNo == 0 || binNo == midBin) { + if (binNo == 0 || binNo == midBin_) { RealType mass = sd->getMass(); Vector3d vel = sd->getVel(); RealType value; switch(rnemdType_) { - case rnemdKinetic : + case rnemdKineticSwap : - value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + - vel[2]*vel[2]); - - if (sd->isDirectional()) { + 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); + 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); + value += angMom[0]*angMom[0]/I(0, 0) + + angMom[1]*angMom[1]/I(1, 1) + + angMom[2]*angMom[2]/I(2, 2); } - } - value = value * 0.5 / OOPSEConstant::energyConvert; + } //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]; @@ -202,7 +402,6 @@ namespace oopse { case rnemdPz : value = mass * vel[2]; break; - case rnemdUnknown : default : break; } @@ -218,7 +417,7 @@ namespace oopse { min_sd = sd; } } - } else { + } else { //midBin_ if (!max_found) { max_val = value; max_sd = sd; @@ -232,99 +431,905 @@ namespace oopse { } } } - //std::cerr << "smallest value = " << min_val << "\n"; - //std::cerr << "largest value = " << max_val << "\n"; - - // missing: swap information in parallel +#ifdef IS_MPI + int nProc, worldRank; + + nProc = MPI::COMM_WORLD.Get_size(); + worldRank = MPI::COMM_WORLD.Get_rank(); + + bool my_min_found = min_found; + bool my_max_found = max_found; + + // Even if we didn't find a minimum, did someone else? + MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR); + // Even if we didn't find a maximum, did someone else? + MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR); +#endif + if (max_found && min_found) { - if (min_val< max_val) { - Vector3d min_vel = min_sd->getVel(); - Vector3d max_vel = max_sd->getVel(); - RealType temp_vel; - switch(rnemdType_) { - case rnemdKinetic : - min_sd->setVel(max_vel); - max_sd->setVel(min_vel); - if (min_sd->isDirectional() && max_sd->isDirectional()) { - Vector3d min_angMom = min_sd->getJ(); - Vector3d max_angMom = max_sd->getJ(); - min_sd->setJ(max_angMom); - max_sd->setJ(min_angMom); - } - break; - case rnemdPx : - temp_vel = min_vel.x(); - min_vel.x() = max_vel.x(); - max_vel.x() = temp_vel; - min_sd->setVel(min_vel); - max_sd->setVel(max_vel); - break; - case rnemdPy : - temp_vel = min_vel.y(); - min_vel.y() = max_vel.y(); - max_vel.y() = temp_vel; - min_sd->setVel(min_vel); - max_sd->setVel(max_vel); - break; - case rnemdPz : - temp_vel = min_vel.z(); - min_vel.z() = max_vel.z(); - max_vel.z() = temp_vel; - min_sd->setVel(min_vel); - max_sd->setVel(max_vel); - break; - case rnemdUnknown : - default : - break; - } - exchangeSum_ += max_val - min_val; - } else { - std::cerr << "exchange NOT performed.\nmin_val > max_val.\n"; + +#ifdef IS_MPI + struct { + RealType val; + int rank; + } max_vals, min_vals; + + if (my_min_found) { + min_vals.val = min_val; + } else { + min_vals.val = HONKING_LARGE_VALUE; } + min_vals.rank = worldRank; + + // Who had the minimum? + MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals, + 1, MPI::REALTYPE_INT, MPI::MINLOC); + min_val = min_vals.val; + + if (my_max_found) { + max_vals.val = max_val; + } else { + max_vals.val = -HONKING_LARGE_VALUE; + } + max_vals.rank = worldRank; + + // Who had the maximum? + MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals, + 1, MPI::REALTYPE_INT, MPI::MAXLOC); + max_val = max_vals.val; +#endif + + if (min_val < max_val) { + +#ifdef IS_MPI + if (max_vals.rank == worldRank && min_vals.rank == worldRank) { + // I have both maximum and minimum, so proceed like a single + // processor version: +#endif + + Vector3d min_vel = min_sd->getVel(); + Vector3d max_vel = max_sd->getVel(); + RealType temp_vel; + + switch(rnemdType_) { + case rnemdKineticSwap : + min_sd->setVel(max_vel); + max_sd->setVel(min_vel); + if (min_sd->isDirectional() && max_sd->isDirectional()) { + Vector3d min_angMom = min_sd->getJ(); + Vector3d max_angMom = max_sd->getJ(); + min_sd->setJ(max_angMom); + max_sd->setJ(min_angMom); + }//angular momenta exchange enabled + //assumes same rigid body identity + break; + case rnemdPx : + temp_vel = min_vel.x(); + min_vel.x() = max_vel.x(); + max_vel.x() = temp_vel; + min_sd->setVel(min_vel); + max_sd->setVel(max_vel); + break; + case rnemdPy : + temp_vel = min_vel.y(); + min_vel.y() = max_vel.y(); + max_vel.y() = temp_vel; + min_sd->setVel(min_vel); + max_sd->setVel(max_vel); + break; + case rnemdPz : + temp_vel = min_vel.z(); + min_vel.z() = max_vel.z(); + max_vel.z() = temp_vel; + min_sd->setVel(min_vel); + max_sd->setVel(max_vel); + break; + default : + break; + } + +#ifdef IS_MPI + // the rest of the cases only apply in parallel simulations: + } else if (max_vals.rank == worldRank) { + // I had the max, but not the minimum + + Vector3d min_vel; + Vector3d max_vel = max_sd->getVel(); + MPI::Status status; + + // point-to-point swap of the velocity vector + MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE, + min_vals.rank, 0, + min_vel.getArrayPointer(), 3, MPI::REALTYPE, + min_vals.rank, 0, status); + + switch(rnemdType_) { + case rnemdKineticSwap : + max_sd->setVel(min_vel); + //angular momenta exchange enabled + if (max_sd->isDirectional()) { + Vector3d min_angMom; + Vector3d max_angMom = max_sd->getJ(); + + // point-to-point swap of the angular momentum vector + MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3, + MPI::REALTYPE, min_vals.rank, 1, + min_angMom.getArrayPointer(), 3, + MPI::REALTYPE, min_vals.rank, 1, + status); + + max_sd->setJ(min_angMom); + } + break; + case rnemdPx : + max_vel.x() = min_vel.x(); + max_sd->setVel(max_vel); + break; + case rnemdPy : + max_vel.y() = min_vel.y(); + max_sd->setVel(max_vel); + break; + case rnemdPz : + max_vel.z() = min_vel.z(); + max_sd->setVel(max_vel); + break; + default : + break; + } + } else if (min_vals.rank == worldRank) { + // I had the minimum but not the maximum: + + Vector3d max_vel; + Vector3d min_vel = min_sd->getVel(); + MPI::Status status; + + // point-to-point swap of the velocity vector + MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE, + max_vals.rank, 0, + max_vel.getArrayPointer(), 3, MPI::REALTYPE, + max_vals.rank, 0, status); + + switch(rnemdType_) { + case rnemdKineticSwap : + min_sd->setVel(max_vel); + //angular momenta exchange enabled + if (min_sd->isDirectional()) { + Vector3d min_angMom = min_sd->getJ(); + Vector3d max_angMom; + + // point-to-point swap of the angular momentum vector + MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3, + MPI::REALTYPE, max_vals.rank, 1, + max_angMom.getArrayPointer(), 3, + MPI::REALTYPE, max_vals.rank, 1, + status); + + min_sd->setJ(max_angMom); + } + break; + case rnemdPx : + min_vel.x() = max_vel.x(); + min_sd->setVel(min_vel); + break; + case rnemdPy : + min_vel.y() = max_vel.y(); + min_sd->setVel(min_vel); + break; + case rnemdPz : + min_vel.z() = max_vel.z(); + min_sd->setVel(min_vel); + break; + default : + break; + } + } +#endif + exchangeSum_ += max_val - min_val; + } else { + sprintf(painCave.errMsg, + "RNEMD: exchange NOT performed because min_val > max_val\n"); + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; + simError(); + failTrialCount_++; + } + } else { + sprintf(painCave.errMsg, + "RNEMD: exchange NOT performed because selected object\n" + "\tnot present in at least one of the two slabs.\n"); + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; + simError(); + failTrialCount_++; + } + + } + + void RNEMD::doScale() { + + Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); + Mat3x3d hmat = currentSnap_->getHmat(); + + seleMan_.setSelectionSet(evaluator_.evaluate()); + + int selei; + StuntDouble* sd; + int idx; + + vector hotBin, coldBin; + + RealType Phx = 0.0; + RealType Phy = 0.0; + RealType Phz = 0.0; + RealType Khx = 0.0; + RealType Khy = 0.0; + RealType Khz = 0.0; + RealType Khw = 0.0; + RealType Pcx = 0.0; + RealType Pcy = 0.0; + RealType Pcz = 0.0; + RealType Kcx = 0.0; + RealType Kcy = 0.0; + RealType Kcz = 0.0; + RealType Kcw = 0.0; + + for (sd = seleMan_.beginSelected(selei); sd != NULL; + sd = seleMan_.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); + } + } + //} + } + } + } + + Khx *= 0.5; + Khy *= 0.5; + Khz *= 0.5; + Khw *= 0.5; + Kcx *= 0.5; + Kcy *= 0.5; + 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); + } else { + c = 1.0 - targetFlux_ / 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) { + x = 1.0 + px * (1.0 - c); + y = 1.0 + py * (1.0 - c); + z = 1.0 + pz * (1.0 - c); + /* more complicated way + w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz + + Khx * px * px + Khy * py * py + Khz * pz * pz) + - 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py) + + Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px) + + Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) + - Kcx - Kcy - Kcz)) / Khw; the following is simpler + */ + 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) + + 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; + } + 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) { + 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) { + vel = (*sdi)->getVel(); + vel.x() *= x; + vel.y() *= y; + vel.z() *= z; + (*sdi)->setVel(vel); + } + if ((*sdi)->isDirectional()) { + Vector3d angMom = (*sdi)->getJ() * w; + //angMom[0] *= w; + //angMom[1] *= w; + //angMom[2] *= w; + (*sdi)->setJ(angMom); + } + } + successfulScale = true; + exchangeSum_ += targetFlux_; + } + } } else { - std::cerr << "exchange NOT performed.\none of the two slabs empty.\n"; + RealType a000, a110, c0, a001, a111, b01, b11, c1; + switch(rnemdType_) { + case rnemdKineticScale : + /* used hotBin coeff's & only scale x & y dimensions + RealType px = Phx / Pcx; + RealType py = Phy / Pcy; + a110 = Khy; + c0 = - Khx - Khy - targetFlux_; + 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_; + 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; + 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_; + break; + case rnemdPxScale : + c = 1 - targetFlux_ / Pcx; + a000 = Kcy; + a110 = Kcz; + c0 = Kcx * c * c - Kcx - Kcy - Kcz; + a001 = py * py * Khy; + a111 = pz * pz * Khz; + b01 = -2.0 * Khy * py * (1.0 + py); + b11 = -2.0 * Khz * pz * (1.0 + pz); + 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; + a000 = Kcx; + a110 = Kcz; + c0 = Kcy * c * c - Kcx - Kcy - Kcz; + a001 = px * px * Khx; + a111 = pz * pz * Khz; + b01 = -2.0 * Khx * px * (1.0 + px); + b11 = -2.0 * Khz * pz * (1.0 + pz); + 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; + a000 = Kcx; + a110 = Kcy; + c0 = Kcz * c * c - Kcx - Kcy - Kcz; + a001 = px * px * Khx; + a111 = py * py * Khy; + b01 = -2.0 * Khx * px * (1.0 + px); + b11 = -2.0 * Khy * py * (1.0 + py); + c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) + + Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0); + break; + default : + break; + } + + RealType v1 = a000 * a111 - a001 * a110; + RealType v2 = a000 * b01; + RealType v3 = a000 * b11; + RealType v4 = a000 * c1 - a001 * c0; + RealType v8 = a110 * b01; + RealType v10 = - b01 * c0; + + RealType u0 = v2 * v10 - v4 * v4; + RealType u1 = -2.0 * v3 * v4; + RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4; + RealType u3 = -2.0 * v1 * v3; + RealType u4 = - v1 * v1; + //rescale coefficients + RealType maxAbs = fabs(u0); + if (maxAbs < fabs(u1)) maxAbs = fabs(u1); + if (maxAbs < fabs(u2)) maxAbs = fabs(u2); + if (maxAbs < fabs(u3)) maxAbs = fabs(u3); + if (maxAbs < fabs(u4)) maxAbs = fabs(u4); + u0 /= maxAbs; + u1 /= maxAbs; + u2 /= maxAbs; + u3 /= maxAbs; + u4 /= maxAbs; + //max_element(start, end) is also available. + Polynomial poly; //same as DoublePolynomial poly; + poly.setCoefficient(4, u4); + poly.setCoefficient(3, u3); + poly.setCoefficient(2, u2); + poly.setCoefficient(1, u1); + poly.setCoefficient(0, u0); + vector realRoots = poly.FindRealRoots(); + + vector::iterator ri; + RealType r1, r2, alpha0; + vector > rps; + 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 ) { + sprintf(painCave.errMsg, + "RNEMD Warning: polynomial solve seems to have an error!"); + painCave.isFatal = 0; + simError(); + failRootCount_++; + } + //might not be useful w/o rescaling coefficients + alpha0 = -c0 - a110 * r2 * r2; + if (alpha0 >= 0.0) { + r1 = sqrt(alpha0 / a000); + if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) + < 1e-6) + { rps.push_back(make_pair(r1, r2)); } + if (r1 > 1e-6) { //r1 non-negative + r1 = -r1; + if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) + < 1e-6) + { rps.push_back(make_pair(r1, r2)); } + } + } + } + // Consider combining together the solving pair part w/ the searching + // best solution part so that we don't need the pairs vector + if (!rps.empty()) { + RealType smallestDiff = HONKING_LARGE_VALUE; + RealType diff; + pair bestPair = make_pair(1.0, 1.0); + vector >::iterator rpi; + for (rpi = rps.begin(); rpi != rps.end(); rpi++) { + r1 = (*rpi).first; + r2 = (*rpi).second; + switch(rnemdType_) { + case rnemdKineticScale : + 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 : + diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); + break; + case rnemdPyScale : + diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + + fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); + break; + case rnemdPzScale : + diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) + + fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); + default : + break; + } + if (diff < smallestDiff) { + smallestDiff = diff; + bestPair = *rpi; + } + } +#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(); +#ifdef IS_MPI + } +#endif + + switch(rnemdType_) { + case rnemdKineticScale : + x = bestPair.first; + y = bestPair.first; + z = bestPair.second; + break; + case rnemdPxScale : + x = c; + y = bestPair.first; + z = bestPair.second; + break; + case rnemdPyScale : + x = bestPair.first; + y = c; + z = bestPair.second; + break; + case rnemdPzScale : + x = bestPair.first; + y = bestPair.second; + z = c; + break; + default : + break; + } + vector::iterator sdi; + Vector3d vel; + for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { + vel = (*sdi)->getVel(); + vel.x() *= x; + vel.y() *= y; + vel.z() *= z; + (*sdi)->setVel(vel); + } + //convert to hotBin coefficient + 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++) { + vel = (*sdi)->getVel(); + vel.x() *= x; + vel.y() *= y; + vel.z() *= z; + (*sdi)->setVel(vel); + } + successfulScale = true; + exchangeSum_ += targetFlux_; + } } - std::cerr << "exchangeSum = " << exchangeSum_ << "\n"; + if (successfulScale != true) { + sprintf(painCave.errMsg, + "RNEMD: exchange NOT performed!\n"); + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; + simError(); + failTrialCount_++; + } } - void RNEMD::getStatus() { - //std::cerr << "in RNEMD!\n"; - //std::cerr << "nBins = " << nBins_ << "\n"; - int midBin = nBins_ / 2; - //std::cerr << "midBin = " << midBin << "\n"; - //std::cerr << "swapTime = " << swapTime_ << "\n"; - //std::cerr << "exchangeSum = " << exchangeSum_ << "\n"; - //std::cerr << "swapType = " << rnemdType_ << "\n"; - //std::cerr << "selection = " << rnemdObjectSelection_ << "\n"; + void RNEMD::doShiftScale() { Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnap_->getHmat(); - //std::cerr << "hmat = " << hmat << "\n"; - seleMan_.setSelectionSet(evaluator_.evaluate()); - //std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n"; + int selei; + StuntDouble* sd; + int idx; + vector hotBin, coldBin; + + Vector3d Ph(V3Zero); + RealType Mh = 0.0; + RealType Kh = 0.0; + Vector3d Pc(V3Zero); + RealType Mc = 0.0; + RealType Kc = 0.0; + + for (sd = seleMan_.beginSelected(selei); sd != NULL; + sd = seleMan_.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); + //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); + } + } + } + } + } + } + + 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, &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); +#endif + + 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(); + if (cNumerator > 0.0) { + RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare(); + 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(); + 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++) { + //vel = (*sdi)->getVel(); + vel = ((*sdi)->getVel() - vc) * c + ac; + (*sdi)->setVel(vel); + if (rnemdType_ == rnemdShiftScaleVAM) { + if ((*sdi)->isDirectional()) { + Vector3d angMom = (*sdi)->getJ() * c; + (*sdi)->setJ(angMom); + } + } + } + for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { + //vel = (*sdi)->getVel(); + vel = ((*sdi)->getVel() - vh) * h + ah; + (*sdi)->setVel(vel); + if (rnemdType_ == rnemdShiftScaleVAM) { + if ((*sdi)->isDirectional()) { + Vector3d angMom = (*sdi)->getJ() * h; + (*sdi)->setJ(angMom); + } + } + } + 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. + } + } + } + } + } + } + } + if (successfulExchange != true) { + sprintf(painCave.errMsg, + "RNEMD: exchange NOT performed!\n"); + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; + simError(); + failTrialCount_++; + } + } + + void RNEMD::doRNEMD() { + + switch(rnemdType_) { + case rnemdKineticScale : + case rnemdKineticScaleVAM : + case rnemdKineticScaleAM : + case rnemdPxScale : + case rnemdPyScale : + case rnemdPzScale : + doScale(); + break; + case rnemdKineticSwap : + case rnemdPx : + case rnemdPy : + case rnemdPz : + doSwap(); + break; + case rnemdShiftScaleV : + case rnemdShiftScaleVAM : + doShiftScale(); + break; + case rnemdUnknown : + default : + break; + } + } + + void RNEMD::collectData() { + + 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; - StuntDouble* min_sd; - RealType max_val; - bool max_found = false; - StuntDouble* max_sd; + // 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)) */ - std::vector valueHist; // keeps track of what's being averaged - std::vector valueCount; // keeps track of the number of degrees of - // freedom being averaged - valueHist.resize(nBins_); - valueCount.resize(nBins_); - //do they initialize themselves to zero automatically? for (sd = seleMan_.beginSelected(selei); sd != NULL; sd = seleMan_.nextSelected(selei)) { @@ -340,73 +1345,247 @@ namespace oopse { // 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_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2)); - - //std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n"; - + 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; + */ RealType mass = sd->getMass(); + mHist_[binNo] += mass; Vector3d vel = sd->getVel(); - //std::cerr << "mass = " << mass << " vel = " << vel << "\n"; RealType value; + //RealType xVal, yVal, zVal; - switch(rnemdType_) { - case rnemdKinetic : - - value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + - vel[2]*vel[2]); - - valueCount[binNo] += 3; - + 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); - - valueCount[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); - valueCount[binNo] +=3; - + 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; } } - //std::cerr <<"this value = " << value << "\n"; - value *= 0.5 / OOPSEConstant::energyConvert; // get it in kcal / mol - value *= 2.0 / OOPSEConstant::kb; // convert to temperature - //std::cerr <<"this value = " << value << "\n"; - break; - case rnemdPx : + value = value / PhysicalConstants::energyConvert + / PhysicalConstants::kb;//may move to getStatus() + tempHist_[binNo] += value; + } + if (outputVx_) { value = mass * vel[0]; - valueCount[binNo]++; - break; - case rnemdPy : + //vxzCount_[binNo]++; + pxzHist_[binNo] += value; + } + if (outputVy_) { value = mass * vel[1]; - valueCount[binNo]++; - break; - case rnemdPz : - value = mass * vel[2]; - valueCount[binNo]++; - break; - case rnemdUnknown : - default : - break; + //vyzCount_[binNo]++; + pyzHist_[binNo] += value; } - //std::cerr << "bin = " << binNo << " value = " << value ; - valueHist[binNo] += value; - //std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n"; + + 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]++; + } + 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; + } + } - - std::cout << counter_++; - for (int j = 0; j < nBins_; j++) - std::cout << "\t" << valueHist[j] / (RealType)valueCount[j]; - std::cout << "\n"; } + + void RNEMD::getStarted() { + 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(); + } + + 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; + +#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 + + if (outputTemp_) { + tempLog_ << time; + for (j = 0; j < rnemdLogWidth_; j++) { + tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j]; + } + tempLog_ << endl; + } + if (outputVx_) { + vxzLog_ << time; + for (j = 0; j < rnemdLogWidth_; j++) { + vxzLog_ << "\t" << pxzHist_[j] / mHist_[j]; + } + vxzLog_ << endl; + } + if (outputVy_) { + vyzLog_ << time; + for (j = 0; j < rnemdLogWidth_; j++) { + vyzLog_ << "\t" << pyzHist_[j] / mHist_[j]; + } + vyzLog_ << endl; + } + + 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; + } + 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; + } + +#ifdef IS_MPI + } +#endif + + for (j = 0; j < rnemdLogWidth_; j++) { + mHist_[j] = 0.0; + } + 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; + } + } } +