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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "integrators/RNEMD.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "primitives/StuntDouble.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/Tuple.hpp" |
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|
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#ifndef IS_MPI |
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#include "math/SeqRandNumGen.hpp" |
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#else |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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|
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/* Remove me after testing*/ |
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/* |
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#include <cstdio> |
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#include <iostream> |
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*/ |
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/*End remove me*/ |
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|
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namespace oopse { |
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|
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RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { |
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|
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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|
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stringToEnumMap_["Kinetic"] = rnemdKinetic; |
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stringToEnumMap_["Px"] = rnemdPx; |
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stringToEnumMap_["Py"] = rnemdPy; |
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stringToEnumMap_["Pz"] = rnemdPz; |
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stringToEnumMap_["Unknown"] = rnemdUnknown; |
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|
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rnemdObjectSelection_ = simParams->getRNEMD_objectSelection(); |
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|
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std::cerr << "calling evaluator with " << rnemdObjectSelection_ << "\n"; |
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evaluator_.loadScriptString(rnemdObjectSelection_); |
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std::cerr << "done\n"; |
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|
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const std::string st = simParams->getRNEMD_swapType(); |
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|
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std::map<std::string, RNEMDTypeEnum>::iterator i; |
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i = stringToEnumMap_.find(st); |
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rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second; |
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|
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set_RNEMD_swapTime(simParams->getRNEMD_swapTime()); |
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set_RNEMD_nBins(simParams->getRNEMD_nBins()); |
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exchangeSum_ = 0.0; |
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counter_ = 0; //added by shenyu |
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//profile_.open("profile", std::ios::out); |
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|
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#ifndef IS_MPI |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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randNumGen_ = new SeqRandNumGen(seedValue); |
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}else { |
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randNumGen_ = new SeqRandNumGen(); |
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} |
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#else |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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randNumGen_ = new ParallelRandNumGen(seedValue); |
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}else { |
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randNumGen_ = new ParallelRandNumGen(); |
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} |
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#endif |
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} |
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|
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RNEMD::~RNEMD() { |
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delete randNumGen_; |
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//profile_.close(); |
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} |
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|
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void RNEMD::doSwap() { |
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//std::cerr << "in RNEMD!\n"; |
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//std::cerr << "nBins = " << nBins_ << "\n"; |
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int midBin = nBins_ / 2; |
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//std::cerr << "midBin = " << midBin << "\n"; |
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//std::cerr << "swapTime = " << swapTime_ << "\n"; |
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//std::cerr << "swapType = " << rnemdType_ << "\n"; |
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//std::cerr << "selection = " << rnemdObjectSelection_ << "\n"; |
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|
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Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d hmat = currentSnap_->getHmat(); |
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|
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//std::cerr << "hmat = " << hmat << "\n"; |
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|
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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|
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//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n"; |
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|
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int selei; |
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StuntDouble* sd; |
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int idx; |
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|
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RealType min_val; |
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bool min_found = false; |
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StuntDouble* min_sd; |
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|
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RealType max_val; |
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bool max_found = false; |
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StuntDouble* max_sd; |
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|
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for (sd = seleMan_.beginSelected(selei); sd != NULL; |
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sd = seleMan_.nextSelected(selei)) { |
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|
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idx = sd->getLocalIndex(); |
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|
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Vector3d pos = sd->getPos(); |
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|
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// wrap the stuntdouble's position back into the box: |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnap_->wrapVector(pos); |
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|
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// which bin is this stuntdouble in? |
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// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
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|
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int binNo = int((nBins_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2)); |
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|
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//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n"; |
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|
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// if we're in bin 0 or the middleBin |
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if (binNo == 0 || binNo == midBin) { |
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|
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RealType mass = sd->getMass(); |
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Vector3d vel = sd->getVel(); |
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RealType value; |
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|
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switch(rnemdType_) { |
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case rnemdKinetic : |
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|
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value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + |
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vel[2]*vel[2]); |
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|
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if (sd->isDirectional()) { |
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Vector3d angMom = sd->getJ(); |
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Mat3x3d I = sd->getI(); |
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|
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if (sd->isLinear()) { |
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int i = sd->linearAxis(); |
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int j = (i + 1) % 3; |
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int k = (i + 2) % 3; |
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value += angMom[j] * angMom[j] / I(j, j) + |
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angMom[k] * angMom[k] / I(k, k); |
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} else { |
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value += angMom[0]*angMom[0]/I(0, 0) |
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+ angMom[1]*angMom[1]/I(1, 1) |
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+ angMom[2]*angMom[2]/I(2, 2); |
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} |
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} |
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value = value * 0.5 / OOPSEConstant::energyConvert; |
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break; |
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case rnemdPx : |
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value = mass * vel[0]; |
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break; |
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case rnemdPy : |
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value = mass * vel[1]; |
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break; |
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case rnemdPz : |
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value = mass * vel[2]; |
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break; |
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case rnemdUnknown : |
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default : |
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break; |
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} |
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|
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if (binNo == 0) { |
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if (!min_found) { |
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min_val = value; |
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min_sd = sd; |
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min_found = true; |
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} else { |
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if (min_val > value) { |
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min_val = value; |
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min_sd = sd; |
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} |
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} |
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} else { |
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if (!max_found) { |
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max_val = value; |
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max_sd = sd; |
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max_found = true; |
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} else { |
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if (max_val < value) { |
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max_val = value; |
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max_sd = sd; |
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} |
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} |
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} |
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} |
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} |
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//std::cerr << "smallest value = " << min_val << "\n"; |
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//std::cerr << "largest value = " << max_val << "\n"; |
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|
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// missing: swap information in parallel |
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|
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if (max_found && min_found) { |
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if (min_val< max_val) { |
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Vector3d min_vel = min_sd->getVel(); |
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Vector3d max_vel = max_sd->getVel(); |
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RealType temp_vel; |
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switch(rnemdType_) { |
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case rnemdKinetic : |
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min_sd->setVel(max_vel); |
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max_sd->setVel(min_vel); |
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if (min_sd->isDirectional() && max_sd->isDirectional()) { |
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Vector3d min_angMom = min_sd->getJ(); |
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Vector3d max_angMom = max_sd->getJ(); |
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min_sd->setJ(max_angMom); |
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max_sd->setJ(min_angMom); |
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} |
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break; |
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case rnemdPx : |
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temp_vel = min_vel.x(); |
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min_vel.x() = max_vel.x(); |
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max_vel.x() = temp_vel; |
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min_sd->setVel(min_vel); |
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max_sd->setVel(max_vel); |
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break; |
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case rnemdPy : |
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temp_vel = min_vel.y(); |
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min_vel.y() = max_vel.y(); |
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max_vel.y() = temp_vel; |
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min_sd->setVel(min_vel); |
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max_sd->setVel(max_vel); |
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break; |
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case rnemdPz : |
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temp_vel = min_vel.z(); |
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min_vel.z() = max_vel.z(); |
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max_vel.z() = temp_vel; |
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min_sd->setVel(min_vel); |
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max_sd->setVel(max_vel); |
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break; |
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case rnemdUnknown : |
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default : |
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break; |
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} |
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exchangeSum_ += max_val - min_val; |
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} else { |
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std::cerr << "exchange NOT performed.\nmin_val > max_val.\n"; |
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} |
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} else { |
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std::cerr << "exchange NOT performed.\none of the two slabs empty.\n"; |
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} |
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std::cerr << "exchangeSum = " << exchangeSum_ << "\n"; |
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} |
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|
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void RNEMD::getStatus() { |
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//std::cerr << "in RNEMD!\n"; |
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//std::cerr << "nBins = " << nBins_ << "\n"; |
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int midBin = nBins_ / 2; |
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//std::cerr << "midBin = " << midBin << "\n"; |
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//std::cerr << "swapTime = " << swapTime_ << "\n"; |
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//std::cerr << "exchangeSum = " << exchangeSum_ << "\n"; |
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//std::cerr << "swapType = " << rnemdType_ << "\n"; |
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//std::cerr << "selection = " << rnemdObjectSelection_ << "\n"; |
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|
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Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d hmat = currentSnap_->getHmat(); |
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|
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//std::cerr << "hmat = " << hmat << "\n"; |
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|
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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|
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//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n"; |
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|
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int selei; |
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StuntDouble* sd; |
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int idx; |
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/* |
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RealType min_val; |
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bool min_found = false; |
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StuntDouble* min_sd; |
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|
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RealType max_val; |
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bool max_found = false; |
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StuntDouble* max_sd; |
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*/ |
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std::vector<RealType> valueHist; // keeps track of what's being averaged |
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std::vector<int> valueCount; // keeps track of the number of degrees of |
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// freedom being averaged |
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valueHist.resize(nBins_); |
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valueCount.resize(nBins_); |
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//do they initialize themselves to zero automatically? |
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for (sd = seleMan_.beginSelected(selei); sd != NULL; |
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sd = seleMan_.nextSelected(selei)) { |
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|
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idx = sd->getLocalIndex(); |
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|
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Vector3d pos = sd->getPos(); |
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|
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// wrap the stuntdouble's position back into the box: |
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|
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if (usePeriodicBoundaryConditions_) |
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currentSnap_->wrapVector(pos); |
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|
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// which bin is this stuntdouble in? |
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// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
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|
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int binNo = int((nBins_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2)); |
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|
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//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n"; |
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|
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RealType mass = sd->getMass(); |
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Vector3d vel = sd->getVel(); |
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//std::cerr << "mass = " << mass << " vel = " << vel << "\n"; |
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RealType value; |
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|
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switch(rnemdType_) { |
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case rnemdKinetic : |
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|
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value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + |
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vel[2]*vel[2]); |
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|
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valueCount[binNo] += 3; |
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|
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if (sd->isDirectional()) { |
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Vector3d angMom = sd->getJ(); |
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Mat3x3d I = sd->getI(); |
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|
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if (sd->isLinear()) { |
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int i = sd->linearAxis(); |
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int j = (i + 1) % 3; |
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int k = (i + 2) % 3; |
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value += angMom[j] * angMom[j] / I(j, j) + |
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angMom[k] * angMom[k] / I(k, k); |
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|
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valueCount[binNo] +=2; |
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|
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} else { |
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value += angMom[0]*angMom[0]/I(0, 0) |
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+ angMom[1]*angMom[1]/I(1, 1) |
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+ angMom[2]*angMom[2]/I(2, 2); |
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valueCount[binNo] +=3; |
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|
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} |
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} |
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//std::cerr <<"this value = " << value << "\n"; |
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value *= 0.5 / OOPSEConstant::energyConvert; // get it in kcal / mol |
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value *= 2.0 / OOPSEConstant::kb; // convert to temperature |
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//std::cerr <<"this value = " << value << "\n"; |
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break; |
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case rnemdPx : |
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value = mass * vel[0]; |
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valueCount[binNo]++; |
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break; |
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case rnemdPy : |
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value = mass * vel[1]; |
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valueCount[binNo]++; |
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break; |
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case rnemdPz : |
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value = mass * vel[2]; |
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valueCount[binNo]++; |
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break; |
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case rnemdUnknown : |
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default : |
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break; |
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} |
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//std::cerr << "bin = " << binNo << " value = " << value ; |
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valueHist[binNo] += value; |
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//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n"; |
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} |
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|
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std::cout << counter_++; |
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for (int j = 0; j < nBins_; j++) |
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std::cout << "\t" << valueHist[j] / (RealType)valueCount[j]; |
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std::cout << "\n"; |
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} |
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} |
