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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <cmath> |
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#include "integrators/RNEMD.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/Vector.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "math/Polynomial.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "primitives/StuntDouble.hpp" |
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#include "utils/PhysicalConstants.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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#include <mpi.h> |
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#endif |
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|
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#define HONKING_LARGE_VALUE 1.0e10 |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), |
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usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { |
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|
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failTrialCount_ = 0; |
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failRootCount_ = 0; |
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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_["KineticSwap"] = rnemdKineticSwap; |
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stringToEnumMap_["KineticScale"] = rnemdKineticScale; |
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stringToEnumMap_["KineticScaleVAM"] = rnemdKineticScaleVAM; |
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stringToEnumMap_["KineticScaleAM"] = rnemdKineticScaleAM; |
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stringToEnumMap_["PxScale"] = rnemdPxScale; |
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stringToEnumMap_["PyScale"] = rnemdPyScale; |
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stringToEnumMap_["PzScale"] = rnemdPzScale; |
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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_["ShiftScaleV"] = rnemdShiftScaleV; |
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stringToEnumMap_["ShiftScaleVAM"] = rnemdShiftScaleVAM; |
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stringToEnumMap_["Unknown"] = rnemdUnknown; |
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|
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runTime_ = simParams->getRunTime(); |
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statusTime_ = simParams->getStatusTime(); |
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|
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rnemdObjectSelection_ = simParams->getRNEMD_objectSelection(); |
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evaluator_.loadScriptString(rnemdObjectSelection_); |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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|
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// do some sanity checking |
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|
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int selectionCount = seleMan_.getSelectionCount(); |
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int nIntegrable = info->getNGlobalIntegrableObjects(); |
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|
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if (selectionCount > nIntegrable) { |
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sprintf(painCave.errMsg, |
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"RNEMD: The current RNEMD_objectSelection,\n" |
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"\t\t%s\n" |
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"\thas resulted in %d selected objects. However,\n" |
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"\tthe total number of integrable objects in the system\n" |
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"\tis only %d. This is almost certainly not what you want\n" |
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"\tto do. A likely cause of this is forgetting the _RB_0\n" |
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"\tselector in the selection script!\n", |
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rnemdObjectSelection_.c_str(), |
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selectionCount, nIntegrable); |
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painCave.isFatal = 0; |
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painCave.severity = OPENMD_WARNING; |
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simError(); |
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} |
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|
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const string st = simParams->getRNEMD_exchangeType(); |
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|
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map<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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if (rnemdType_ == rnemdUnknown) { |
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sprintf(painCave.errMsg, |
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"RNEMD: The current RNEMD_exchangeType,\n" |
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"\t\t%s\n" |
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"\tis not one of the recognized exchange types.\n", |
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st.c_str()); |
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painCave.isFatal = 1; |
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painCave.severity = OPENMD_ERROR; |
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simError(); |
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} |
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|
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outputTemp_ = false; |
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if (simParams->haveRNEMD_outputTemperature()) { |
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outputTemp_ = simParams->getRNEMD_outputTemperature(); |
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} else if ((rnemdType_ == rnemdKineticSwap) || |
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(rnemdType_ == rnemdKineticScale) || |
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(rnemdType_ == rnemdKineticScaleVAM) || |
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(rnemdType_ == rnemdKineticScaleAM)) { |
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outputTemp_ = true; |
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} |
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outputVx_ = false; |
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if (simParams->haveRNEMD_outputVx()) { |
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outputVx_ = simParams->getRNEMD_outputVx(); |
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} else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) { |
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outputVx_ = true; |
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} |
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outputVy_ = false; |
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if (simParams->haveRNEMD_outputVy()) { |
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outputVy_ = simParams->getRNEMD_outputVy(); |
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} else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) { |
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outputVy_ = true; |
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} |
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output3DTemp_ = false; |
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if (simParams->haveRNEMD_outputXyzTemperature()) { |
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output3DTemp_ = simParams->getRNEMD_outputXyzTemperature(); |
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} |
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outputRotTemp_ = false; |
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if (simParams->haveRNEMD_outputRotTemperature()) { |
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outputRotTemp_ = simParams->getRNEMD_outputRotTemperature(); |
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} |
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// James put this in. |
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outputDen_ = false; |
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if (simParams->haveRNEMD_outputDen()) { |
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outputDen_ = simParams->getRNEMD_outputDen(); |
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} |
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outputAh_ = false; |
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if (simParams->haveRNEMD_outputAh()) { |
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outputAh_ = simParams->getRNEMD_outputAh(); |
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} |
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outputVz_ = false; |
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if (simParams->haveRNEMD_outputVz()) { |
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outputVz_ = simParams->getRNEMD_outputVz(); |
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} else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) { |
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outputVz_ = true; |
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} |
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|
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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|
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//may have rnemdWriter separately |
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string rnemdFileName; |
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|
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if (outputTemp_) { |
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rnemdFileName = "temperature.log"; |
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tempLog_.open(rnemdFileName.c_str()); |
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} |
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if (outputVx_) { |
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rnemdFileName = "velocityX.log"; |
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vxzLog_.open(rnemdFileName.c_str()); |
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} |
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if (outputVy_) { |
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rnemdFileName = "velocityY.log"; |
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vyzLog_.open(rnemdFileName.c_str()); |
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} |
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|
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if (output3DTemp_) { |
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rnemdFileName = "temperatureX.log"; |
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xTempLog_.open(rnemdFileName.c_str()); |
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rnemdFileName = "temperatureY.log"; |
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yTempLog_.open(rnemdFileName.c_str()); |
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rnemdFileName = "temperatureZ.log"; |
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zTempLog_.open(rnemdFileName.c_str()); |
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} |
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if (outputRotTemp_) { |
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rnemdFileName = "temperatureR.log"; |
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rotTempLog_.open(rnemdFileName.c_str()); |
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} |
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|
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//James put this in |
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if (outputDen_) { |
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rnemdFileName = "Density.log"; |
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denLog_.open(rnemdFileName.c_str()); |
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} |
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if (outputAh_) { |
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rnemdFileName = "Ah.log"; |
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AhLog_.open(rnemdFileName.c_str()); |
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} |
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if (outputVz_) { |
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rnemdFileName = "velocityZ.log"; |
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vzzLog_.open(rnemdFileName.c_str()); |
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} |
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logFrameCount_ = 0; |
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#ifdef IS_MPI |
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} |
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#endif |
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|
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set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime()); |
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set_RNEMD_nBins(simParams->getRNEMD_nBins()); |
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midBin_ = nBins_ / 2; |
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if (simParams->haveRNEMD_binShift()) { |
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if (simParams->getRNEMD_binShift()) { |
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zShift_ = 0.5 / (RealType)(nBins_); |
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} else { |
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zShift_ = 0.0; |
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} |
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} else { |
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zShift_ = 0.0; |
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} |
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//cerr << "I shift slabs by " << zShift_ << " Lz\n"; |
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//shift slabs by half slab width, maybe useful in heterogeneous systems |
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//set to 0.0 if not using it; N/A in status output yet |
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if (simParams->haveRNEMD_logWidth()) { |
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set_RNEMD_logWidth(simParams->getRNEMD_logWidth()); |
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/*arbitary rnemdLogWidth_, no checking; |
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if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) { |
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cerr << "WARNING! RNEMD_logWidth has abnormal value!\n"; |
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cerr << "Automaically set back to default.\n"; |
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rnemdLogWidth_ = nBins_; |
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}*/ |
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} else { |
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set_RNEMD_logWidth(nBins_); |
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} |
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tempHist_.resize(rnemdLogWidth_, 0.0); |
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tempCount_.resize(rnemdLogWidth_, 0); |
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pxzHist_.resize(rnemdLogWidth_, 0.0); |
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//vxzCount_.resize(rnemdLogWidth_, 0); |
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pyzHist_.resize(rnemdLogWidth_, 0.0); |
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//vyzCount_.resize(rnemdLogWidth_, 0); |
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|
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mHist_.resize(rnemdLogWidth_, 0.0); |
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xTempHist_.resize(rnemdLogWidth_, 0.0); |
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yTempHist_.resize(rnemdLogWidth_, 0.0); |
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zTempHist_.resize(rnemdLogWidth_, 0.0); |
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xyzTempCount_.resize(rnemdLogWidth_, 0); |
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rotTempHist_.resize(rnemdLogWidth_, 0.0); |
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rotTempCount_.resize(rnemdLogWidth_, 0); |
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// James put this in |
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DenHist_.resize(rnemdLogWidth_, 0.0); |
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pzzHist_.resize(rnemdLogWidth_, 0.0); |
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|
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set_RNEMD_exchange_total(0.0); |
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if (simParams->haveRNEMD_targetFlux()) { |
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set_RNEMD_target_flux(simParams->getRNEMD_targetFlux()); |
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} else { |
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set_RNEMD_target_flux(0.0); |
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} |
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if (simParams->haveRNEMD_targetJzKE()) { |
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set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE()); |
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} else { |
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set_RNEMD_target_JzKE(0.0); |
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} |
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if (simParams->haveRNEMD_targetJzpx()) { |
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set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx()); |
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} else { |
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set_RNEMD_target_jzpx(0.0); |
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} |
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jzp_.x() = targetJzpx_; |
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njzp_.x() = -targetJzpx_; |
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if (simParams->haveRNEMD_targetJzpy()) { |
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set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy()); |
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} else { |
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set_RNEMD_target_jzpy(0.0); |
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} |
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jzp_.y() = targetJzpy_; |
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njzp_.y() = -targetJzpy_; |
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if (simParams->haveRNEMD_targetJzpz()) { |
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set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz()); |
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} else { |
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set_RNEMD_target_jzpz(0.0); |
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} |
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jzp_.z() = targetJzpz_; |
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njzp_.z() = -targetJzpz_; |
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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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|
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#ifdef IS_MPI |
| 327 |
if (worldRank == 0) { |
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#endif |
| 329 |
|
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sprintf(painCave.errMsg, |
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"RNEMD: total failed trials: %d\n", |
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failTrialCount_); |
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painCave.isFatal = 0; |
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painCave.severity = OPENMD_INFO; |
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simError(); |
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|
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if (outputTemp_) tempLog_.close(); |
| 338 |
if (outputVx_) vxzLog_.close(); |
| 339 |
if (outputVy_) vyzLog_.close(); |
| 340 |
|
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if (rnemdType_ == rnemdKineticScale || rnemdType_ == rnemdPxScale || |
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rnemdType_ == rnemdPyScale) { |
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sprintf(painCave.errMsg, |
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"RNEMD: total root-checking warnings: %d\n", |
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failRootCount_); |
| 346 |
painCave.isFatal = 0; |
| 347 |
painCave.severity = OPENMD_INFO; |
| 348 |
simError(); |
| 349 |
} |
| 350 |
if (output3DTemp_) { |
| 351 |
xTempLog_.close(); |
| 352 |
yTempLog_.close(); |
| 353 |
zTempLog_.close(); |
| 354 |
} |
| 355 |
if (outputRotTemp_) rotTempLog_.close(); |
| 356 |
// James put this in |
| 357 |
if (outputDen_) denLog_.close(); |
| 358 |
if (outputAh_) AhLog_.close(); |
| 359 |
if (outputVz_) vzzLog_.close(); |
| 360 |
|
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#ifdef IS_MPI |
| 362 |
} |
| 363 |
#endif |
| 364 |
} |
| 365 |
|
| 366 |
void RNEMD::doSwap() { |
| 367 |
|
| 368 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 369 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 370 |
|
| 371 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 372 |
|
| 373 |
int selei; |
| 374 |
StuntDouble* sd; |
| 375 |
int idx; |
| 376 |
|
| 377 |
RealType min_val; |
| 378 |
bool min_found = false; |
| 379 |
StuntDouble* min_sd; |
| 380 |
|
| 381 |
RealType max_val; |
| 382 |
bool max_found = false; |
| 383 |
StuntDouble* max_sd; |
| 384 |
|
| 385 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 386 |
sd = seleMan_.nextSelected(selei)) { |
| 387 |
|
| 388 |
idx = sd->getLocalIndex(); |
| 389 |
|
| 390 |
Vector3d pos = sd->getPos(); |
| 391 |
|
| 392 |
// wrap the stuntdouble's position back into the box: |
| 393 |
|
| 394 |
if (usePeriodicBoundaryConditions_) |
| 395 |
currentSnap_->wrapVector(pos); |
| 396 |
|
| 397 |
// which bin is this stuntdouble in? |
| 398 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 399 |
|
| 400 |
int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; |
| 401 |
|
| 402 |
|
| 403 |
// if we're in bin 0 or the middleBin |
| 404 |
if (binNo == 0 || binNo == midBin_) { |
| 405 |
|
| 406 |
RealType mass = sd->getMass(); |
| 407 |
Vector3d vel = sd->getVel(); |
| 408 |
RealType value; |
| 409 |
|
| 410 |
switch(rnemdType_) { |
| 411 |
case rnemdKineticSwap : |
| 412 |
|
| 413 |
value = mass * vel.lengthSquare(); |
| 414 |
|
| 415 |
if (sd->isDirectional()) { |
| 416 |
Vector3d angMom = sd->getJ(); |
| 417 |
Mat3x3d I = sd->getI(); |
| 418 |
|
| 419 |
if (sd->isLinear()) { |
| 420 |
int i = sd->linearAxis(); |
| 421 |
int j = (i + 1) % 3; |
| 422 |
int k = (i + 2) % 3; |
| 423 |
value += angMom[j] * angMom[j] / I(j, j) + |
| 424 |
angMom[k] * angMom[k] / I(k, k); |
| 425 |
} else { |
| 426 |
value += angMom[0]*angMom[0]/I(0, 0) |
| 427 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 428 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 429 |
} |
| 430 |
} //angular momenta exchange enabled |
| 431 |
//energyConvert temporarily disabled |
| 432 |
//make exchangeSum_ comparable between swap & scale |
| 433 |
//value = value * 0.5 / PhysicalConstants::energyConvert; |
| 434 |
value *= 0.5; |
| 435 |
break; |
| 436 |
case rnemdPx : |
| 437 |
value = mass * vel[0]; |
| 438 |
break; |
| 439 |
case rnemdPy : |
| 440 |
value = mass * vel[1]; |
| 441 |
break; |
| 442 |
case rnemdPz : |
| 443 |
value = mass * vel[2]; |
| 444 |
break; |
| 445 |
default : |
| 446 |
break; |
| 447 |
} |
| 448 |
|
| 449 |
if (binNo == 0) { |
| 450 |
if (!min_found) { |
| 451 |
min_val = value; |
| 452 |
min_sd = sd; |
| 453 |
min_found = true; |
| 454 |
} else { |
| 455 |
if (min_val > value) { |
| 456 |
min_val = value; |
| 457 |
min_sd = sd; |
| 458 |
} |
| 459 |
} |
| 460 |
} else { //midBin_ |
| 461 |
if (!max_found) { |
| 462 |
max_val = value; |
| 463 |
max_sd = sd; |
| 464 |
max_found = true; |
| 465 |
} else { |
| 466 |
if (max_val < value) { |
| 467 |
max_val = value; |
| 468 |
max_sd = sd; |
| 469 |
} |
| 470 |
} |
| 471 |
} |
| 472 |
} |
| 473 |
} |
| 474 |
|
| 475 |
#ifdef IS_MPI |
| 476 |
int nProc, worldRank; |
| 477 |
|
| 478 |
nProc = MPI::COMM_WORLD.Get_size(); |
| 479 |
worldRank = MPI::COMM_WORLD.Get_rank(); |
| 480 |
|
| 481 |
bool my_min_found = min_found; |
| 482 |
bool my_max_found = max_found; |
| 483 |
|
| 484 |
// Even if we didn't find a minimum, did someone else? |
| 485 |
MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR); |
| 486 |
// Even if we didn't find a maximum, did someone else? |
| 487 |
MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR); |
| 488 |
#endif |
| 489 |
|
| 490 |
if (max_found && min_found) { |
| 491 |
|
| 492 |
#ifdef IS_MPI |
| 493 |
struct { |
| 494 |
RealType val; |
| 495 |
int rank; |
| 496 |
} max_vals, min_vals; |
| 497 |
|
| 498 |
if (my_min_found) { |
| 499 |
min_vals.val = min_val; |
| 500 |
} else { |
| 501 |
min_vals.val = HONKING_LARGE_VALUE; |
| 502 |
} |
| 503 |
min_vals.rank = worldRank; |
| 504 |
|
| 505 |
// Who had the minimum? |
| 506 |
MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals, |
| 507 |
1, MPI::REALTYPE_INT, MPI::MINLOC); |
| 508 |
min_val = min_vals.val; |
| 509 |
|
| 510 |
if (my_max_found) { |
| 511 |
max_vals.val = max_val; |
| 512 |
} else { |
| 513 |
max_vals.val = -HONKING_LARGE_VALUE; |
| 514 |
} |
| 515 |
max_vals.rank = worldRank; |
| 516 |
|
| 517 |
// Who had the maximum? |
| 518 |
MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals, |
| 519 |
1, MPI::REALTYPE_INT, MPI::MAXLOC); |
| 520 |
max_val = max_vals.val; |
| 521 |
#endif |
| 522 |
|
| 523 |
if (min_val < max_val) { |
| 524 |
|
| 525 |
#ifdef IS_MPI |
| 526 |
if (max_vals.rank == worldRank && min_vals.rank == worldRank) { |
| 527 |
// I have both maximum and minimum, so proceed like a single |
| 528 |
// processor version: |
| 529 |
#endif |
| 530 |
|
| 531 |
Vector3d min_vel = min_sd->getVel(); |
| 532 |
Vector3d max_vel = max_sd->getVel(); |
| 533 |
RealType temp_vel; |
| 534 |
|
| 535 |
switch(rnemdType_) { |
| 536 |
case rnemdKineticSwap : |
| 537 |
min_sd->setVel(max_vel); |
| 538 |
max_sd->setVel(min_vel); |
| 539 |
if (min_sd->isDirectional() && max_sd->isDirectional()) { |
| 540 |
Vector3d min_angMom = min_sd->getJ(); |
| 541 |
Vector3d max_angMom = max_sd->getJ(); |
| 542 |
min_sd->setJ(max_angMom); |
| 543 |
max_sd->setJ(min_angMom); |
| 544 |
}//angular momenta exchange enabled |
| 545 |
//assumes same rigid body identity |
| 546 |
break; |
| 547 |
case rnemdPx : |
| 548 |
temp_vel = min_vel.x(); |
| 549 |
min_vel.x() = max_vel.x(); |
| 550 |
max_vel.x() = temp_vel; |
| 551 |
min_sd->setVel(min_vel); |
| 552 |
max_sd->setVel(max_vel); |
| 553 |
break; |
| 554 |
case rnemdPy : |
| 555 |
temp_vel = min_vel.y(); |
| 556 |
min_vel.y() = max_vel.y(); |
| 557 |
max_vel.y() = temp_vel; |
| 558 |
min_sd->setVel(min_vel); |
| 559 |
max_sd->setVel(max_vel); |
| 560 |
break; |
| 561 |
case rnemdPz : |
| 562 |
temp_vel = min_vel.z(); |
| 563 |
min_vel.z() = max_vel.z(); |
| 564 |
max_vel.z() = temp_vel; |
| 565 |
min_sd->setVel(min_vel); |
| 566 |
max_sd->setVel(max_vel); |
| 567 |
break; |
| 568 |
default : |
| 569 |
break; |
| 570 |
} |
| 571 |
|
| 572 |
#ifdef IS_MPI |
| 573 |
// the rest of the cases only apply in parallel simulations: |
| 574 |
} else if (max_vals.rank == worldRank) { |
| 575 |
// I had the max, but not the minimum |
| 576 |
|
| 577 |
Vector3d min_vel; |
| 578 |
Vector3d max_vel = max_sd->getVel(); |
| 579 |
MPI::Status status; |
| 580 |
|
| 581 |
// point-to-point swap of the velocity vector |
| 582 |
MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 583 |
min_vals.rank, 0, |
| 584 |
min_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 585 |
min_vals.rank, 0, status); |
| 586 |
|
| 587 |
switch(rnemdType_) { |
| 588 |
case rnemdKineticSwap : |
| 589 |
max_sd->setVel(min_vel); |
| 590 |
//angular momenta exchange enabled |
| 591 |
if (max_sd->isDirectional()) { |
| 592 |
Vector3d min_angMom; |
| 593 |
Vector3d max_angMom = max_sd->getJ(); |
| 594 |
|
| 595 |
// point-to-point swap of the angular momentum vector |
| 596 |
MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3, |
| 597 |
MPI::REALTYPE, min_vals.rank, 1, |
| 598 |
min_angMom.getArrayPointer(), 3, |
| 599 |
MPI::REALTYPE, min_vals.rank, 1, |
| 600 |
status); |
| 601 |
|
| 602 |
max_sd->setJ(min_angMom); |
| 603 |
} |
| 604 |
break; |
| 605 |
case rnemdPx : |
| 606 |
max_vel.x() = min_vel.x(); |
| 607 |
max_sd->setVel(max_vel); |
| 608 |
break; |
| 609 |
case rnemdPy : |
| 610 |
max_vel.y() = min_vel.y(); |
| 611 |
max_sd->setVel(max_vel); |
| 612 |
break; |
| 613 |
case rnemdPz : |
| 614 |
max_vel.z() = min_vel.z(); |
| 615 |
max_sd->setVel(max_vel); |
| 616 |
break; |
| 617 |
default : |
| 618 |
break; |
| 619 |
} |
| 620 |
} else if (min_vals.rank == worldRank) { |
| 621 |
// I had the minimum but not the maximum: |
| 622 |
|
| 623 |
Vector3d max_vel; |
| 624 |
Vector3d min_vel = min_sd->getVel(); |
| 625 |
MPI::Status status; |
| 626 |
|
| 627 |
// point-to-point swap of the velocity vector |
| 628 |
MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 629 |
max_vals.rank, 0, |
| 630 |
max_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 631 |
max_vals.rank, 0, status); |
| 632 |
|
| 633 |
switch(rnemdType_) { |
| 634 |
case rnemdKineticSwap : |
| 635 |
min_sd->setVel(max_vel); |
| 636 |
//angular momenta exchange enabled |
| 637 |
if (min_sd->isDirectional()) { |
| 638 |
Vector3d min_angMom = min_sd->getJ(); |
| 639 |
Vector3d max_angMom; |
| 640 |
|
| 641 |
// point-to-point swap of the angular momentum vector |
| 642 |
MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3, |
| 643 |
MPI::REALTYPE, max_vals.rank, 1, |
| 644 |
max_angMom.getArrayPointer(), 3, |
| 645 |
MPI::REALTYPE, max_vals.rank, 1, |
| 646 |
status); |
| 647 |
|
| 648 |
min_sd->setJ(max_angMom); |
| 649 |
} |
| 650 |
break; |
| 651 |
case rnemdPx : |
| 652 |
min_vel.x() = max_vel.x(); |
| 653 |
min_sd->setVel(min_vel); |
| 654 |
break; |
| 655 |
case rnemdPy : |
| 656 |
min_vel.y() = max_vel.y(); |
| 657 |
min_sd->setVel(min_vel); |
| 658 |
break; |
| 659 |
case rnemdPz : |
| 660 |
min_vel.z() = max_vel.z(); |
| 661 |
min_sd->setVel(min_vel); |
| 662 |
break; |
| 663 |
default : |
| 664 |
break; |
| 665 |
} |
| 666 |
} |
| 667 |
#endif |
| 668 |
exchangeSum_ += max_val - min_val; |
| 669 |
} else { |
| 670 |
sprintf(painCave.errMsg, |
| 671 |
"RNEMD: exchange NOT performed because min_val > max_val\n"); |
| 672 |
painCave.isFatal = 0; |
| 673 |
painCave.severity = OPENMD_INFO; |
| 674 |
simError(); |
| 675 |
failTrialCount_++; |
| 676 |
} |
| 677 |
} else { |
| 678 |
sprintf(painCave.errMsg, |
| 679 |
"RNEMD: exchange NOT performed because selected object\n" |
| 680 |
"\tnot present in at least one of the two slabs.\n"); |
| 681 |
painCave.isFatal = 0; |
| 682 |
painCave.severity = OPENMD_INFO; |
| 683 |
simError(); |
| 684 |
failTrialCount_++; |
| 685 |
} |
| 686 |
|
| 687 |
} |
| 688 |
|
| 689 |
void RNEMD::doScale() { |
| 690 |
|
| 691 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 692 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 693 |
|
| 694 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 695 |
|
| 696 |
int selei; |
| 697 |
StuntDouble* sd; |
| 698 |
int idx; |
| 699 |
|
| 700 |
vector<StuntDouble*> hotBin, coldBin; |
| 701 |
|
| 702 |
RealType Phx = 0.0; |
| 703 |
RealType Phy = 0.0; |
| 704 |
RealType Phz = 0.0; |
| 705 |
RealType Khx = 0.0; |
| 706 |
RealType Khy = 0.0; |
| 707 |
RealType Khz = 0.0; |
| 708 |
RealType Khw = 0.0; |
| 709 |
RealType Pcx = 0.0; |
| 710 |
RealType Pcy = 0.0; |
| 711 |
RealType Pcz = 0.0; |
| 712 |
RealType Kcx = 0.0; |
| 713 |
RealType Kcy = 0.0; |
| 714 |
RealType Kcz = 0.0; |
| 715 |
RealType Kcw = 0.0; |
| 716 |
|
| 717 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 718 |
sd = seleMan_.nextSelected(selei)) { |
| 719 |
|
| 720 |
idx = sd->getLocalIndex(); |
| 721 |
|
| 722 |
Vector3d pos = sd->getPos(); |
| 723 |
|
| 724 |
// wrap the stuntdouble's position back into the box: |
| 725 |
|
| 726 |
if (usePeriodicBoundaryConditions_) |
| 727 |
currentSnap_->wrapVector(pos); |
| 728 |
|
| 729 |
// which bin is this stuntdouble in? |
| 730 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 731 |
|
| 732 |
int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; |
| 733 |
|
| 734 |
// if we're in bin 0 or the middleBin |
| 735 |
if (binNo == 0 || binNo == midBin_) { |
| 736 |
|
| 737 |
RealType mass = sd->getMass(); |
| 738 |
Vector3d vel = sd->getVel(); |
| 739 |
|
| 740 |
if (binNo == 0) { |
| 741 |
hotBin.push_back(sd); |
| 742 |
Phx += mass * vel.x(); |
| 743 |
Phy += mass * vel.y(); |
| 744 |
Phz += mass * vel.z(); |
| 745 |
Khx += mass * vel.x() * vel.x(); |
| 746 |
Khy += mass * vel.y() * vel.y(); |
| 747 |
Khz += mass * vel.z() * vel.z(); |
| 748 |
//if (rnemdType_ == rnemdKineticScaleVAM) { |
| 749 |
if (sd->isDirectional()) { |
| 750 |
Vector3d angMom = sd->getJ(); |
| 751 |
Mat3x3d I = sd->getI(); |
| 752 |
if (sd->isLinear()) { |
| 753 |
int i = sd->linearAxis(); |
| 754 |
int j = (i + 1) % 3; |
| 755 |
int k = (i + 2) % 3; |
| 756 |
Khw += angMom[j] * angMom[j] / I(j, j) + |
| 757 |
angMom[k] * angMom[k] / I(k, k); |
| 758 |
} else { |
| 759 |
Khw += angMom[0]*angMom[0]/I(0, 0) |
| 760 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 761 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 762 |
} |
| 763 |
} |
| 764 |
//} |
| 765 |
} else { //midBin_ |
| 766 |
coldBin.push_back(sd); |
| 767 |
Pcx += mass * vel.x(); |
| 768 |
Pcy += mass * vel.y(); |
| 769 |
Pcz += mass * vel.z(); |
| 770 |
Kcx += mass * vel.x() * vel.x(); |
| 771 |
Kcy += mass * vel.y() * vel.y(); |
| 772 |
Kcz += mass * vel.z() * vel.z(); |
| 773 |
//if (rnemdType_ == rnemdKineticScaleVAM) { |
| 774 |
if (sd->isDirectional()) { |
| 775 |
Vector3d angMom = sd->getJ(); |
| 776 |
Mat3x3d I = sd->getI(); |
| 777 |
if (sd->isLinear()) { |
| 778 |
int i = sd->linearAxis(); |
| 779 |
int j = (i + 1) % 3; |
| 780 |
int k = (i + 2) % 3; |
| 781 |
Kcw += angMom[j] * angMom[j] / I(j, j) + |
| 782 |
angMom[k] * angMom[k] / I(k, k); |
| 783 |
} else { |
| 784 |
Kcw += angMom[0]*angMom[0]/I(0, 0) |
| 785 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 786 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 787 |
} |
| 788 |
} |
| 789 |
//} |
| 790 |
} |
| 791 |
} |
| 792 |
} |
| 793 |
|
| 794 |
Khx *= 0.5; |
| 795 |
Khy *= 0.5; |
| 796 |
Khz *= 0.5; |
| 797 |
Khw *= 0.5; |
| 798 |
Kcx *= 0.5; |
| 799 |
Kcy *= 0.5; |
| 800 |
Kcz *= 0.5; |
| 801 |
Kcw *= 0.5; |
| 802 |
|
| 803 |
// std::cerr << "Khx= " << Khx << "\tKhy= " << Khy << "\tKhz= " << Khz |
| 804 |
// << "\tKhw= " << Khw << "\tKcx= " << Kcx << "\tKcy= " << Kcy |
| 805 |
// << "\tKcz= " << Kcz << "\tKcw= " << Kcw << "\n"; |
| 806 |
// std::cerr << "Phx= " << Phx << "\tPhy= " << Phy << "\tPhz= " << Phz |
| 807 |
// << "\tPcx= " << Pcx << "\tPcy= " << Pcy << "\tPcz= " <<Pcz<<"\n"; |
| 808 |
|
| 809 |
#ifdef IS_MPI |
| 810 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM); |
| 811 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM); |
| 812 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM); |
| 813 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM); |
| 814 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM); |
| 815 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM); |
| 816 |
|
| 817 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM); |
| 818 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM); |
| 819 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM); |
| 820 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM); |
| 821 |
|
| 822 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM); |
| 823 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM); |
| 824 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM); |
| 825 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM); |
| 826 |
#endif |
| 827 |
|
| 828 |
//solve coldBin coeff's first |
| 829 |
RealType px = Pcx / Phx; |
| 830 |
RealType py = Pcy / Phy; |
| 831 |
RealType pz = Pcz / Phz; |
| 832 |
RealType c, x, y, z; |
| 833 |
bool successfulScale = false; |
| 834 |
if ((rnemdType_ == rnemdKineticScaleVAM) || |
| 835 |
(rnemdType_ == rnemdKineticScaleAM)) { |
| 836 |
//may need sanity check Khw & Kcw > 0 |
| 837 |
|
| 838 |
if (rnemdType_ == rnemdKineticScaleVAM) { |
| 839 |
c = 1.0 - targetFlux_ / (Kcx + Kcy + Kcz + Kcw); |
| 840 |
} else { |
| 841 |
c = 1.0 - targetFlux_ / Kcw; |
| 842 |
} |
| 843 |
|
| 844 |
if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients |
| 845 |
c = sqrt(c); |
| 846 |
std::cerr << "cold slab scaling coefficient: " << c << endl; |
| 847 |
//now convert to hotBin coefficient |
| 848 |
RealType w = 0.0; |
| 849 |
if (rnemdType_ == rnemdKineticScaleVAM) { |
| 850 |
x = 1.0 + px * (1.0 - c); |
| 851 |
y = 1.0 + py * (1.0 - c); |
| 852 |
z = 1.0 + pz * (1.0 - c); |
| 853 |
/* more complicated way |
| 854 |
w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz |
| 855 |
+ Khx * px * px + Khy * py * py + Khz * pz * pz) |
| 856 |
- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py) |
| 857 |
+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px) |
| 858 |
+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) |
| 859 |
- Kcx - Kcy - Kcz)) / Khw; the following is simpler |
| 860 |
*/ |
| 861 |
if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) && |
| 862 |
(fabs(z - 1.0) < 0.1)) { |
| 863 |
w = 1.0 + (targetFlux_ + Khx * (1.0 - x * x) + Khy * (1.0 - y * y) |
| 864 |
+ Khz * (1.0 - z * z)) / Khw; |
| 865 |
}//no need to calculate w if x, y or z is out of range |
| 866 |
} else { |
| 867 |
w = 1.0 + targetFlux_ / Khw; |
| 868 |
} |
| 869 |
if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients |
| 870 |
//if w is in the right range, so should be x, y, z. |
| 871 |
vector<StuntDouble*>::iterator sdi; |
| 872 |
Vector3d vel; |
| 873 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 874 |
if (rnemdType_ == rnemdKineticScaleVAM) { |
| 875 |
vel = (*sdi)->getVel() * c; |
| 876 |
//vel.x() *= c; |
| 877 |
//vel.y() *= c; |
| 878 |
//vel.z() *= c; |
| 879 |
(*sdi)->setVel(vel); |
| 880 |
} |
| 881 |
if ((*sdi)->isDirectional()) { |
| 882 |
Vector3d angMom = (*sdi)->getJ() * c; |
| 883 |
//angMom[0] *= c; |
| 884 |
//angMom[1] *= c; |
| 885 |
//angMom[2] *= c; |
| 886 |
(*sdi)->setJ(angMom); |
| 887 |
} |
| 888 |
} |
| 889 |
w = sqrt(w); |
| 890 |
std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z |
| 891 |
<< "\twh= " << w << endl; |
| 892 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 893 |
if (rnemdType_ == rnemdKineticScaleVAM) { |
| 894 |
vel = (*sdi)->getVel(); |
| 895 |
vel.x() *= x; |
| 896 |
vel.y() *= y; |
| 897 |
vel.z() *= z; |
| 898 |
(*sdi)->setVel(vel); |
| 899 |
} |
| 900 |
if ((*sdi)->isDirectional()) { |
| 901 |
Vector3d angMom = (*sdi)->getJ() * w; |
| 902 |
//angMom[0] *= w; |
| 903 |
//angMom[1] *= w; |
| 904 |
//angMom[2] *= w; |
| 905 |
(*sdi)->setJ(angMom); |
| 906 |
} |
| 907 |
} |
| 908 |
successfulScale = true; |
| 909 |
exchangeSum_ += targetFlux_; |
| 910 |
} |
| 911 |
} |
| 912 |
} else { |
| 913 |
RealType a000, a110, c0, a001, a111, b01, b11, c1; |
| 914 |
switch(rnemdType_) { |
| 915 |
case rnemdKineticScale : |
| 916 |
/* used hotBin coeff's & only scale x & y dimensions |
| 917 |
RealType px = Phx / Pcx; |
| 918 |
RealType py = Phy / Pcy; |
| 919 |
a110 = Khy; |
| 920 |
c0 = - Khx - Khy - targetFlux_; |
| 921 |
a000 = Khx; |
| 922 |
a111 = Kcy * py * py; |
| 923 |
b11 = -2.0 * Kcy * py * (1.0 + py); |
| 924 |
c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + targetFlux_; |
| 925 |
b01 = -2.0 * Kcx * px * (1.0 + px); |
| 926 |
a001 = Kcx * px * px; |
| 927 |
*/ |
| 928 |
//scale all three dimensions, let c_x = c_y |
| 929 |
a000 = Kcx + Kcy; |
| 930 |
a110 = Kcz; |
| 931 |
c0 = targetFlux_ - Kcx - Kcy - Kcz; |
| 932 |
a001 = Khx * px * px + Khy * py * py; |
| 933 |
a111 = Khz * pz * pz; |
| 934 |
b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)); |
| 935 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 936 |
c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) |
| 937 |
+ Khz * pz * (2.0 + pz) - targetFlux_; |
| 938 |
break; |
| 939 |
case rnemdPxScale : |
| 940 |
c = 1 - targetFlux_ / Pcx; |
| 941 |
a000 = Kcy; |
| 942 |
a110 = Kcz; |
| 943 |
c0 = Kcx * c * c - Kcx - Kcy - Kcz; |
| 944 |
a001 = py * py * Khy; |
| 945 |
a111 = pz * pz * Khz; |
| 946 |
b01 = -2.0 * Khy * py * (1.0 + py); |
| 947 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 948 |
c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) |
| 949 |
+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0); |
| 950 |
break; |
| 951 |
case rnemdPyScale : |
| 952 |
c = 1 - targetFlux_ / Pcy; |
| 953 |
a000 = Kcx; |
| 954 |
a110 = Kcz; |
| 955 |
c0 = Kcy * c * c - Kcx - Kcy - Kcz; |
| 956 |
a001 = px * px * Khx; |
| 957 |
a111 = pz * pz * Khz; |
| 958 |
b01 = -2.0 * Khx * px * (1.0 + px); |
| 959 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 960 |
c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz) |
| 961 |
+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0); |
| 962 |
break; |
| 963 |
case rnemdPzScale ://we don't really do this, do we? |
| 964 |
c = 1 - targetFlux_ / Pcz; |
| 965 |
a000 = Kcx; |
| 966 |
a110 = Kcy; |
| 967 |
c0 = Kcz * c * c - Kcx - Kcy - Kcz; |
| 968 |
a001 = px * px * Khx; |
| 969 |
a111 = py * py * Khy; |
| 970 |
b01 = -2.0 * Khx * px * (1.0 + px); |
| 971 |
b11 = -2.0 * Khy * py * (1.0 + py); |
| 972 |
c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) |
| 973 |
+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0); |
| 974 |
break; |
| 975 |
default : |
| 976 |
break; |
| 977 |
} |
| 978 |
|
| 979 |
RealType v1 = a000 * a111 - a001 * a110; |
| 980 |
RealType v2 = a000 * b01; |
| 981 |
RealType v3 = a000 * b11; |
| 982 |
RealType v4 = a000 * c1 - a001 * c0; |
| 983 |
RealType v8 = a110 * b01; |
| 984 |
RealType v10 = - b01 * c0; |
| 985 |
|
| 986 |
RealType u0 = v2 * v10 - v4 * v4; |
| 987 |
RealType u1 = -2.0 * v3 * v4; |
| 988 |
RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4; |
| 989 |
RealType u3 = -2.0 * v1 * v3; |
| 990 |
RealType u4 = - v1 * v1; |
| 991 |
//rescale coefficients |
| 992 |
RealType maxAbs = fabs(u0); |
| 993 |
if (maxAbs < fabs(u1)) maxAbs = fabs(u1); |
| 994 |
if (maxAbs < fabs(u2)) maxAbs = fabs(u2); |
| 995 |
if (maxAbs < fabs(u3)) maxAbs = fabs(u3); |
| 996 |
if (maxAbs < fabs(u4)) maxAbs = fabs(u4); |
| 997 |
u0 /= maxAbs; |
| 998 |
u1 /= maxAbs; |
| 999 |
u2 /= maxAbs; |
| 1000 |
u3 /= maxAbs; |
| 1001 |
u4 /= maxAbs; |
| 1002 |
//max_element(start, end) is also available. |
| 1003 |
Polynomial<RealType> poly; //same as DoublePolynomial poly; |
| 1004 |
poly.setCoefficient(4, u4); |
| 1005 |
poly.setCoefficient(3, u3); |
| 1006 |
poly.setCoefficient(2, u2); |
| 1007 |
poly.setCoefficient(1, u1); |
| 1008 |
poly.setCoefficient(0, u0); |
| 1009 |
vector<RealType> realRoots = poly.FindRealRoots(); |
| 1010 |
|
| 1011 |
vector<RealType>::iterator ri; |
| 1012 |
RealType r1, r2, alpha0; |
| 1013 |
vector<pair<RealType,RealType> > rps; |
| 1014 |
for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) { |
| 1015 |
r2 = *ri; |
| 1016 |
//check if FindRealRoots() give the right answer |
| 1017 |
if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { |
| 1018 |
sprintf(painCave.errMsg, |
| 1019 |
"RNEMD Warning: polynomial solve seems to have an error!"); |
| 1020 |
painCave.isFatal = 0; |
| 1021 |
simError(); |
| 1022 |
failRootCount_++; |
| 1023 |
} |
| 1024 |
//might not be useful w/o rescaling coefficients |
| 1025 |
alpha0 = -c0 - a110 * r2 * r2; |
| 1026 |
if (alpha0 >= 0.0) { |
| 1027 |
r1 = sqrt(alpha0 / a000); |
| 1028 |
if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) |
| 1029 |
< 1e-6) |
| 1030 |
{ rps.push_back(make_pair(r1, r2)); } |
| 1031 |
if (r1 > 1e-6) { //r1 non-negative |
| 1032 |
r1 = -r1; |
| 1033 |
if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) |
| 1034 |
< 1e-6) |
| 1035 |
{ rps.push_back(make_pair(r1, r2)); } |
| 1036 |
} |
| 1037 |
} |
| 1038 |
} |
| 1039 |
// Consider combining together the solving pair part w/ the searching |
| 1040 |
// best solution part so that we don't need the pairs vector |
| 1041 |
if (!rps.empty()) { |
| 1042 |
RealType smallestDiff = HONKING_LARGE_VALUE; |
| 1043 |
RealType diff; |
| 1044 |
pair<RealType,RealType> bestPair = make_pair(1.0, 1.0); |
| 1045 |
vector<pair<RealType,RealType> >::iterator rpi; |
| 1046 |
for (rpi = rps.begin(); rpi != rps.end(); rpi++) { |
| 1047 |
r1 = (*rpi).first; |
| 1048 |
r2 = (*rpi).second; |
| 1049 |
switch(rnemdType_) { |
| 1050 |
case rnemdKineticScale : |
| 1051 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1052 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2) |
| 1053 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); |
| 1054 |
break; |
| 1055 |
case rnemdPxScale : |
| 1056 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1057 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); |
| 1058 |
break; |
| 1059 |
case rnemdPyScale : |
| 1060 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1061 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); |
| 1062 |
break; |
| 1063 |
case rnemdPzScale : |
| 1064 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1065 |
+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); |
| 1066 |
default : |
| 1067 |
break; |
| 1068 |
} |
| 1069 |
if (diff < smallestDiff) { |
| 1070 |
smallestDiff = diff; |
| 1071 |
bestPair = *rpi; |
| 1072 |
} |
| 1073 |
} |
| 1074 |
#ifdef IS_MPI |
| 1075 |
if (worldRank == 0) { |
| 1076 |
#endif |
| 1077 |
sprintf(painCave.errMsg, |
| 1078 |
"RNEMD: roots r1= %lf\tr2 = %lf\n", |
| 1079 |
bestPair.first, bestPair.second); |
| 1080 |
painCave.isFatal = 0; |
| 1081 |
painCave.severity = OPENMD_INFO; |
| 1082 |
simError(); |
| 1083 |
#ifdef IS_MPI |
| 1084 |
} |
| 1085 |
#endif |
| 1086 |
|
| 1087 |
switch(rnemdType_) { |
| 1088 |
case rnemdKineticScale : |
| 1089 |
x = bestPair.first; |
| 1090 |
y = bestPair.first; |
| 1091 |
z = bestPair.second; |
| 1092 |
break; |
| 1093 |
case rnemdPxScale : |
| 1094 |
x = c; |
| 1095 |
y = bestPair.first; |
| 1096 |
z = bestPair.second; |
| 1097 |
break; |
| 1098 |
case rnemdPyScale : |
| 1099 |
x = bestPair.first; |
| 1100 |
y = c; |
| 1101 |
z = bestPair.second; |
| 1102 |
break; |
| 1103 |
case rnemdPzScale : |
| 1104 |
x = bestPair.first; |
| 1105 |
y = bestPair.second; |
| 1106 |
z = c; |
| 1107 |
break; |
| 1108 |
default : |
| 1109 |
break; |
| 1110 |
} |
| 1111 |
vector<StuntDouble*>::iterator sdi; |
| 1112 |
Vector3d vel; |
| 1113 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1114 |
vel = (*sdi)->getVel(); |
| 1115 |
vel.x() *= x; |
| 1116 |
vel.y() *= y; |
| 1117 |
vel.z() *= z; |
| 1118 |
(*sdi)->setVel(vel); |
| 1119 |
} |
| 1120 |
//convert to hotBin coefficient |
| 1121 |
x = 1.0 + px * (1.0 - x); |
| 1122 |
y = 1.0 + py * (1.0 - y); |
| 1123 |
z = 1.0 + pz * (1.0 - z); |
| 1124 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1125 |
vel = (*sdi)->getVel(); |
| 1126 |
vel.x() *= x; |
| 1127 |
vel.y() *= y; |
| 1128 |
vel.z() *= z; |
| 1129 |
(*sdi)->setVel(vel); |
| 1130 |
} |
| 1131 |
successfulScale = true; |
| 1132 |
exchangeSum_ += targetFlux_; |
| 1133 |
} |
| 1134 |
} |
| 1135 |
if (successfulScale != true) { |
| 1136 |
sprintf(painCave.errMsg, |
| 1137 |
"RNEMD: exchange NOT performed!\n"); |
| 1138 |
painCave.isFatal = 0; |
| 1139 |
painCave.severity = OPENMD_INFO; |
| 1140 |
simError(); |
| 1141 |
failTrialCount_++; |
| 1142 |
} |
| 1143 |
} |
| 1144 |
|
| 1145 |
void RNEMD::doShiftScale() { |
| 1146 |
|
| 1147 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1148 |
RealType time = currentSnap_->getTime(); |
| 1149 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1150 |
|
| 1151 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 1152 |
|
| 1153 |
int selei; |
| 1154 |
StuntDouble* sd; |
| 1155 |
int idx; |
| 1156 |
|
| 1157 |
vector<StuntDouble*> hotBin, coldBin; |
| 1158 |
|
| 1159 |
Vector3d Ph(V3Zero); |
| 1160 |
RealType Mh = 0.0; |
| 1161 |
RealType Kh = 0.0; |
| 1162 |
Vector3d Pc(V3Zero); |
| 1163 |
RealType Mc = 0.0; |
| 1164 |
RealType Kc = 0.0; |
| 1165 |
|
| 1166 |
|
| 1167 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 1168 |
sd = seleMan_.nextSelected(selei)) { |
| 1169 |
|
| 1170 |
idx = sd->getLocalIndex(); |
| 1171 |
|
| 1172 |
Vector3d pos = sd->getPos(); |
| 1173 |
|
| 1174 |
// wrap the stuntdouble's position back into the box: |
| 1175 |
|
| 1176 |
if (usePeriodicBoundaryConditions_) |
| 1177 |
currentSnap_->wrapVector(pos); |
| 1178 |
|
| 1179 |
// which bin is this stuntdouble in? |
| 1180 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 1181 |
|
| 1182 |
int binNo = int(nBins_ * (pos.z() / hmat(2,2) + zShift_ + 0.5)) % nBins_; |
| 1183 |
|
| 1184 |
// if we're in bin 0 or the middleBin |
| 1185 |
if (binNo == 0 || binNo == midBin_) { |
| 1186 |
|
| 1187 |
RealType mass = sd->getMass(); |
| 1188 |
Vector3d vel = sd->getVel(); |
| 1189 |
|
| 1190 |
if (binNo == 0) { |
| 1191 |
hotBin.push_back(sd); |
| 1192 |
//std::cerr << "before, velocity = " << vel << endl; |
| 1193 |
Ph += mass * vel; |
| 1194 |
//std::cerr << "after, velocity = " << vel << endl; |
| 1195 |
Mh += mass; |
| 1196 |
Kh += mass * vel.lengthSquare(); |
| 1197 |
if (rnemdType_ == rnemdShiftScaleVAM) { |
| 1198 |
if (sd->isDirectional()) { |
| 1199 |
Vector3d angMom = sd->getJ(); |
| 1200 |
Mat3x3d I = sd->getI(); |
| 1201 |
if (sd->isLinear()) { |
| 1202 |
int i = sd->linearAxis(); |
| 1203 |
int j = (i + 1) % 3; |
| 1204 |
int k = (i + 2) % 3; |
| 1205 |
Kh += angMom[j] * angMom[j] / I(j, j) + |
| 1206 |
angMom[k] * angMom[k] / I(k, k); |
| 1207 |
} else { |
| 1208 |
Kh += angMom[0] * angMom[0] / I(0, 0) + |
| 1209 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1210 |
angMom[2] * angMom[2] / I(2, 2); |
| 1211 |
} |
| 1212 |
} |
| 1213 |
} |
| 1214 |
} else { //midBin_ |
| 1215 |
coldBin.push_back(sd); |
| 1216 |
Pc += mass * vel; |
| 1217 |
Mc += mass; |
| 1218 |
Kc += mass * vel.lengthSquare(); |
| 1219 |
if (rnemdType_ == rnemdShiftScaleVAM) { |
| 1220 |
if (sd->isDirectional()) { |
| 1221 |
Vector3d angMom = sd->getJ(); |
| 1222 |
Mat3x3d I = sd->getI(); |
| 1223 |
if (sd->isLinear()) { |
| 1224 |
int i = sd->linearAxis(); |
| 1225 |
int j = (i + 1) % 3; |
| 1226 |
int k = (i + 2) % 3; |
| 1227 |
Kc += angMom[j] * angMom[j] / I(j, j) + |
| 1228 |
angMom[k] * angMom[k] / I(k, k); |
| 1229 |
} else { |
| 1230 |
Kc += angMom[0] * angMom[0] / I(0, 0) + |
| 1231 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1232 |
angMom[2] * angMom[2] / I(2, 2); |
| 1233 |
} |
| 1234 |
} |
| 1235 |
} |
| 1236 |
} |
| 1237 |
} |
| 1238 |
} |
| 1239 |
|
| 1240 |
Kh *= 0.5; |
| 1241 |
Kc *= 0.5; |
| 1242 |
|
| 1243 |
// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc |
| 1244 |
// << "\tKc= " << Kc << endl; |
| 1245 |
// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl; |
| 1246 |
|
| 1247 |
#ifdef IS_MPI |
| 1248 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1249 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1250 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM); |
| 1251 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM); |
| 1252 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM); |
| 1253 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM); |
| 1254 |
#endif |
| 1255 |
|
| 1256 |
bool successfulExchange = false; |
| 1257 |
if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty |
| 1258 |
Vector3d vc = Pc / Mc; |
| 1259 |
Vector3d ac = njzp_ / Mc + vc; |
| 1260 |
Vector3d acrec = njzp_ / Mc; |
| 1261 |
RealType cNumerator = Kc - targetJzKE_ - 0.5 * Mc * ac.lengthSquare(); |
| 1262 |
if (cNumerator > 0.0) { |
| 1263 |
RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare(); |
| 1264 |
if (cDenominator > 0.0) { |
| 1265 |
RealType c = sqrt(cNumerator / cDenominator); |
| 1266 |
if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients |
| 1267 |
Vector3d vh = Ph / Mh; |
| 1268 |
Vector3d ah = jzp_ / Mh + vh; |
| 1269 |
Vector3d ahrec = jzp_ / Mh; |
| 1270 |
RealType hNumerator = Kh + targetJzKE_ |
| 1271 |
- 0.5 * Mh * ah.lengthSquare(); |
| 1272 |
if (hNumerator > 0.0) { |
| 1273 |
RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare(); |
| 1274 |
if (hDenominator > 0.0) { |
| 1275 |
RealType h = sqrt(hNumerator / hDenominator); |
| 1276 |
if ((h > 0.9) && (h < 1.1)) { |
| 1277 |
// std::cerr << "cold slab scaling coefficient: " << c << "\n"; |
| 1278 |
// std::cerr << "hot slab scaling coefficient: " << h << "\n"; |
| 1279 |
vector<StuntDouble*>::iterator sdi; |
| 1280 |
Vector3d vel; |
| 1281 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1282 |
//vel = (*sdi)->getVel(); |
| 1283 |
vel = ((*sdi)->getVel() - vc) * c + ac; |
| 1284 |
(*sdi)->setVel(vel); |
| 1285 |
if (rnemdType_ == rnemdShiftScaleVAM) { |
| 1286 |
if ((*sdi)->isDirectional()) { |
| 1287 |
Vector3d angMom = (*sdi)->getJ() * c; |
| 1288 |
(*sdi)->setJ(angMom); |
| 1289 |
} |
| 1290 |
} |
| 1291 |
} |
| 1292 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1293 |
//vel = (*sdi)->getVel(); |
| 1294 |
vel = ((*sdi)->getVel() - vh) * h + ah; |
| 1295 |
(*sdi)->setVel(vel); |
| 1296 |
if (rnemdType_ == rnemdShiftScaleVAM) { |
| 1297 |
if ((*sdi)->isDirectional()) { |
| 1298 |
Vector3d angMom = (*sdi)->getJ() * h; |
| 1299 |
(*sdi)->setJ(angMom); |
| 1300 |
} |
| 1301 |
} |
| 1302 |
} |
| 1303 |
successfulExchange = true; |
| 1304 |
exchangeSum_ += targetFlux_; |
| 1305 |
// this is a redundant variable for doShiftScale() so that |
| 1306 |
// RNEMD can output one exchange quantity needed in a job. |
| 1307 |
// need a better way to do this. |
| 1308 |
//cerr << "acx =" << ac.x() << "ahx =" << ah.x() << '\n'; |
| 1309 |
//cerr << "acy =" << ac.y() << "ahy =" << ah.y() << '\n'; |
| 1310 |
//cerr << "acz =" << ac.z() << "ahz =" << ah.z() << '\n'; |
| 1311 |
Asum_ += (ahrec.z() - acrec.z()); |
| 1312 |
Jsum_ += (jzp_.z()*((1/Mh)+(1/Mc))); |
| 1313 |
AhCount_ = ahrec.z(); |
| 1314 |
if (outputAh_) { |
| 1315 |
AhLog_ << time << " "; |
| 1316 |
AhLog_ << AhCount_; |
| 1317 |
AhLog_ << endl; |
| 1318 |
} |
| 1319 |
} |
| 1320 |
} |
| 1321 |
} |
| 1322 |
} |
| 1323 |
} |
| 1324 |
} |
| 1325 |
} |
| 1326 |
if (successfulExchange != true) { |
| 1327 |
// sprintf(painCave.errMsg, |
| 1328 |
// "RNEMD: exchange NOT performed!\n"); |
| 1329 |
// painCave.isFatal = 0; |
| 1330 |
// painCave.severity = OPENMD_INFO; |
| 1331 |
// simError(); |
| 1332 |
failTrialCount_++; |
| 1333 |
} |
| 1334 |
} |
| 1335 |
|
| 1336 |
void RNEMD::doRNEMD() { |
| 1337 |
|
| 1338 |
switch(rnemdType_) { |
| 1339 |
case rnemdKineticScale : |
| 1340 |
case rnemdKineticScaleVAM : |
| 1341 |
case rnemdKineticScaleAM : |
| 1342 |
case rnemdPxScale : |
| 1343 |
case rnemdPyScale : |
| 1344 |
case rnemdPzScale : |
| 1345 |
doScale(); |
| 1346 |
break; |
| 1347 |
case rnemdKineticSwap : |
| 1348 |
case rnemdPx : |
| 1349 |
case rnemdPy : |
| 1350 |
case rnemdPz : |
| 1351 |
doSwap(); |
| 1352 |
break; |
| 1353 |
case rnemdShiftScaleV : |
| 1354 |
case rnemdShiftScaleVAM : |
| 1355 |
doShiftScale(); |
| 1356 |
break; |
| 1357 |
case rnemdUnknown : |
| 1358 |
default : |
| 1359 |
break; |
| 1360 |
} |
| 1361 |
} |
| 1362 |
|
| 1363 |
void RNEMD::collectData() { |
| 1364 |
|
| 1365 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1366 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1367 |
|
| 1368 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 1369 |
|
| 1370 |
int selei; |
| 1371 |
StuntDouble* sd; |
| 1372 |
int idx; |
| 1373 |
|
| 1374 |
logFrameCount_++; |
| 1375 |
|
| 1376 |
// alternative approach, track all molecules instead of only those |
| 1377 |
// selected for scaling/swapping: |
| 1378 |
/* |
| 1379 |
SimInfo::MoleculeIterator miter; |
| 1380 |
vector<StuntDouble*>::iterator iiter; |
| 1381 |
Molecule* mol; |
| 1382 |
StuntDouble* integrableObject; |
| 1383 |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 1384 |
mol = info_->nextMolecule(miter)) |
| 1385 |
integrableObject is essentially sd |
| 1386 |
for (integrableObject = mol->beginIntegrableObject(iiter); |
| 1387 |
integrableObject != NULL; |
| 1388 |
integrableObject = mol->nextIntegrableObject(iiter)) |
| 1389 |
*/ |
| 1390 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 1391 |
sd = seleMan_.nextSelected(selei)) { |
| 1392 |
|
| 1393 |
idx = sd->getLocalIndex(); |
| 1394 |
|
| 1395 |
Vector3d pos = sd->getPos(); |
| 1396 |
|
| 1397 |
// wrap the stuntdouble's position back into the box: |
| 1398 |
|
| 1399 |
if (usePeriodicBoundaryConditions_) |
| 1400 |
currentSnap_->wrapVector(pos); |
| 1401 |
|
| 1402 |
// which bin is this stuntdouble in? |
| 1403 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 1404 |
|
| 1405 |
int binNo = int(rnemdLogWidth_ * (pos.z() / hmat(2,2) + 0.5)) % |
| 1406 |
rnemdLogWidth_; |
| 1407 |
// no symmetrization allowed due to arbitary rnemdLogWidth_ |
| 1408 |
/* |
| 1409 |
if (rnemdLogWidth_ == midBin_ + 1) |
| 1410 |
if (binNo > midBin_) |
| 1411 |
binNo = nBins_ - binNo; |
| 1412 |
*/ |
| 1413 |
RealType mass = sd->getMass(); |
| 1414 |
mHist_[binNo] += mass; |
| 1415 |
Vector3d vel = sd->getVel(); |
| 1416 |
RealType value; |
| 1417 |
//RealType xVal, yVal, zVal; |
| 1418 |
|
| 1419 |
if (outputTemp_) { |
| 1420 |
value = mass * vel.lengthSquare(); |
| 1421 |
tempCount_[binNo] += 3; |
| 1422 |
if (sd->isDirectional()) { |
| 1423 |
Vector3d angMom = sd->getJ(); |
| 1424 |
Mat3x3d I = sd->getI(); |
| 1425 |
if (sd->isLinear()) { |
| 1426 |
int i = sd->linearAxis(); |
| 1427 |
int j = (i + 1) % 3; |
| 1428 |
int k = (i + 2) % 3; |
| 1429 |
value += angMom[j] * angMom[j] / I(j, j) + |
| 1430 |
angMom[k] * angMom[k] / I(k, k); |
| 1431 |
tempCount_[binNo] +=2; |
| 1432 |
} else { |
| 1433 |
value += angMom[0] * angMom[0] / I(0, 0) + |
| 1434 |
angMom[1]*angMom[1]/I(1, 1) + |
| 1435 |
angMom[2]*angMom[2]/I(2, 2); |
| 1436 |
tempCount_[binNo] +=3; |
| 1437 |
} |
| 1438 |
} |
| 1439 |
value = value / PhysicalConstants::energyConvert |
| 1440 |
/ PhysicalConstants::kb;//may move to getStatus() |
| 1441 |
tempHist_[binNo] += value; |
| 1442 |
} |
| 1443 |
if (outputVx_) { |
| 1444 |
value = mass * vel[0]; |
| 1445 |
//vxzCount_[binNo]++; |
| 1446 |
pxzHist_[binNo] += value; |
| 1447 |
} |
| 1448 |
if (outputVy_) { |
| 1449 |
value = mass * vel[1]; |
| 1450 |
//vyzCount_[binNo]++; |
| 1451 |
pyzHist_[binNo] += value; |
| 1452 |
} |
| 1453 |
|
| 1454 |
if (output3DTemp_) { |
| 1455 |
value = mass * vel.x() * vel.x(); |
| 1456 |
xTempHist_[binNo] += value; |
| 1457 |
value = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert |
| 1458 |
/ PhysicalConstants::kb; |
| 1459 |
yTempHist_[binNo] += value; |
| 1460 |
value = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert |
| 1461 |
/ PhysicalConstants::kb; |
| 1462 |
zTempHist_[binNo] += value; |
| 1463 |
xyzTempCount_[binNo]++; |
| 1464 |
} |
| 1465 |
if (outputRotTemp_) { |
| 1466 |
if (sd->isDirectional()) { |
| 1467 |
Vector3d angMom = sd->getJ(); |
| 1468 |
Mat3x3d I = sd->getI(); |
| 1469 |
if (sd->isLinear()) { |
| 1470 |
int i = sd->linearAxis(); |
| 1471 |
int j = (i + 1) % 3; |
| 1472 |
int k = (i + 2) % 3; |
| 1473 |
value = angMom[j] * angMom[j] / I(j, j) + |
| 1474 |
angMom[k] * angMom[k] / I(k, k); |
| 1475 |
rotTempCount_[binNo] +=2; |
| 1476 |
} else { |
| 1477 |
value = angMom[0] * angMom[0] / I(0, 0) + |
| 1478 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1479 |
angMom[2] * angMom[2] / I(2, 2); |
| 1480 |
rotTempCount_[binNo] +=3; |
| 1481 |
} |
| 1482 |
} |
| 1483 |
value = value / PhysicalConstants::energyConvert |
| 1484 |
/ PhysicalConstants::kb;//may move to getStatus() |
| 1485 |
rotTempHist_[binNo] += value; |
| 1486 |
} |
| 1487 |
// James put this in. |
| 1488 |
if (outputDen_) { |
| 1489 |
//value = 1.0; |
| 1490 |
DenHist_[binNo] += 1; |
| 1491 |
} |
| 1492 |
if (outputVz_) { |
| 1493 |
value = mass * vel[2]; |
| 1494 |
//vyzCount_[binNo]++; |
| 1495 |
pzzHist_[binNo] += value; |
| 1496 |
} |
| 1497 |
} |
| 1498 |
} |
| 1499 |
|
| 1500 |
void RNEMD::getStarted() { |
| 1501 |
collectData(); |
| 1502 |
/*now can output profile in step 0, but might not be useful; |
| 1503 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1504 |
Stats& stat = currentSnap_->statData; |
| 1505 |
stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_; |
| 1506 |
*/ |
| 1507 |
//may output a header for the log file here |
| 1508 |
getStatus(); |
| 1509 |
} |
| 1510 |
|
| 1511 |
void RNEMD::getStatus() { |
| 1512 |
|
| 1513 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1514 |
Stats& stat = currentSnap_->statData; |
| 1515 |
RealType time = currentSnap_->getTime(); |
| 1516 |
|
| 1517 |
stat[Stats::RNEMD_EXCHANGE_TOTAL] = exchangeSum_; |
| 1518 |
//or to be more meaningful, define another item as exchangeSum_ / time |
| 1519 |
int j; |
| 1520 |
|
| 1521 |
#ifdef IS_MPI |
| 1522 |
|
| 1523 |
// all processors have the same number of bins, and STL vectors pack their |
| 1524 |
// arrays, so in theory, this should be safe: |
| 1525 |
|
| 1526 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &mHist_[0], |
| 1527 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1528 |
if (outputTemp_) { |
| 1529 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempHist_[0], |
| 1530 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1531 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &tempCount_[0], |
| 1532 |
rnemdLogWidth_, MPI::INT, MPI::SUM); |
| 1533 |
} |
| 1534 |
if (outputVx_) { |
| 1535 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pxzHist_[0], |
| 1536 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1537 |
//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vxzCount_[0], |
| 1538 |
// rnemdLogWidth_, MPI::INT, MPI::SUM); |
| 1539 |
} |
| 1540 |
if (outputVy_) { |
| 1541 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pyzHist_[0], |
| 1542 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1543 |
//MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &vyzCount_[0], |
| 1544 |
// rnemdLogWidth_, MPI::INT, MPI::SUM); |
| 1545 |
} |
| 1546 |
if (output3DTemp_) { |
| 1547 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xTempHist_[0], |
| 1548 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1549 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &yTempHist_[0], |
| 1550 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1551 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &zTempHist_[0], |
| 1552 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1553 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &xyzTempCount_[0], |
| 1554 |
rnemdLogWidth_, MPI::INT, MPI::SUM); |
| 1555 |
} |
| 1556 |
if (outputRotTemp_) { |
| 1557 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempHist_[0], |
| 1558 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1559 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &rotTempCount_[0], |
| 1560 |
rnemdLogWidth_, MPI::INT, MPI::SUM); |
| 1561 |
} |
| 1562 |
// James put this in |
| 1563 |
if (outputDen_) { |
| 1564 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &DenHist_[0], |
| 1565 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1566 |
} |
| 1567 |
if (outputAh_) { |
| 1568 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &AhCount_, |
| 1569 |
1, MPI::REALTYPE, MPI::SUM); |
| 1570 |
} |
| 1571 |
if (outputVz_) { |
| 1572 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pzzHist_[0], |
| 1573 |
rnemdLogWidth_, MPI::REALTYPE, MPI::SUM); |
| 1574 |
} |
| 1575 |
|
| 1576 |
// If we're the root node, should we print out the results |
| 1577 |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 1578 |
if (worldRank == 0) { |
| 1579 |
#endif |
| 1580 |
|
| 1581 |
if (outputTemp_) { |
| 1582 |
tempLog_ << time; |
| 1583 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1584 |
tempLog_ << "\t" << tempHist_[j] / (RealType)tempCount_[j]; |
| 1585 |
} |
| 1586 |
tempLog_ << endl; |
| 1587 |
} |
| 1588 |
if (outputVx_) { |
| 1589 |
vxzLog_ << time; |
| 1590 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1591 |
vxzLog_ << "\t" << pxzHist_[j] / mHist_[j]; |
| 1592 |
} |
| 1593 |
vxzLog_ << endl; |
| 1594 |
} |
| 1595 |
if (outputVy_) { |
| 1596 |
vyzLog_ << time; |
| 1597 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1598 |
vyzLog_ << "\t" << pyzHist_[j] / mHist_[j]; |
| 1599 |
} |
| 1600 |
vyzLog_ << endl; |
| 1601 |
} |
| 1602 |
|
| 1603 |
if (output3DTemp_) { |
| 1604 |
RealType temp; |
| 1605 |
xTempLog_ << time; |
| 1606 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1607 |
if (outputVx_) |
| 1608 |
xTempHist_[j] -= pxzHist_[j] * pxzHist_[j] / mHist_[j]; |
| 1609 |
temp = xTempHist_[j] / (RealType)xyzTempCount_[j] |
| 1610 |
/ PhysicalConstants::energyConvert / PhysicalConstants::kb; |
| 1611 |
xTempLog_ << "\t" << temp; |
| 1612 |
} |
| 1613 |
xTempLog_ << endl; |
| 1614 |
yTempLog_ << time; |
| 1615 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1616 |
yTempLog_ << "\t" << yTempHist_[j] / (RealType)xyzTempCount_[j]; |
| 1617 |
} |
| 1618 |
yTempLog_ << endl; |
| 1619 |
zTempLog_ << time; |
| 1620 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1621 |
zTempLog_ << "\t" << zTempHist_[j] / (RealType)xyzTempCount_[j]; |
| 1622 |
} |
| 1623 |
zTempLog_ << endl; |
| 1624 |
} |
| 1625 |
if (outputRotTemp_) { |
| 1626 |
rotTempLog_ << time; |
| 1627 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1628 |
rotTempLog_ << "\t" << rotTempHist_[j] / (RealType)rotTempCount_[j]; |
| 1629 |
} |
| 1630 |
rotTempLog_ << endl; |
| 1631 |
} |
| 1632 |
// James put this in. |
| 1633 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1634 |
if (outputDen_) { |
| 1635 |
denLog_ << time; |
| 1636 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1637 |
|
| 1638 |
RealType binVol = hmat(0,0) * hmat(1,1) * (hmat(2,2) / float(nBins_)); |
| 1639 |
denLog_ << "\t" << DenHist_[j] / (float(logFrameCount_) * binVol); |
| 1640 |
} |
| 1641 |
denLog_ << endl; |
| 1642 |
} |
| 1643 |
if (outputVz_) { |
| 1644 |
vzzLog_ << time; |
| 1645 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1646 |
vzzLog_ << "\t" << pzzHist_[j] / mHist_[j]; |
| 1647 |
} |
| 1648 |
vzzLog_ << endl; |
| 1649 |
} |
| 1650 |
#ifdef IS_MPI |
| 1651 |
} |
| 1652 |
#endif |
| 1653 |
|
| 1654 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1655 |
mHist_[j] = 0.0; |
| 1656 |
} |
| 1657 |
if (outputTemp_) |
| 1658 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1659 |
tempCount_[j] = 0; |
| 1660 |
tempHist_[j] = 0.0; |
| 1661 |
} |
| 1662 |
if (outputVx_) |
| 1663 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1664 |
//pxzCount_[j] = 0; |
| 1665 |
pxzHist_[j] = 0.0; |
| 1666 |
} |
| 1667 |
if (outputVy_) |
| 1668 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1669 |
//pyzCount_[j] = 0; |
| 1670 |
pyzHist_[j] = 0.0; |
| 1671 |
} |
| 1672 |
|
| 1673 |
if (output3DTemp_) |
| 1674 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1675 |
xTempHist_[j] = 0.0; |
| 1676 |
yTempHist_[j] = 0.0; |
| 1677 |
zTempHist_[j] = 0.0; |
| 1678 |
xyzTempCount_[j] = 0; |
| 1679 |
} |
| 1680 |
if (outputRotTemp_) |
| 1681 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1682 |
rotTempCount_[j] = 0; |
| 1683 |
rotTempHist_[j] = 0.0; |
| 1684 |
} |
| 1685 |
// James put this in |
| 1686 |
if (outputDen_) |
| 1687 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1688 |
//pyzCount_[j] = 0; |
| 1689 |
DenHist_[j] = 0.0; |
| 1690 |
} |
| 1691 |
if (outputVz_) |
| 1692 |
for (j = 0; j < rnemdLogWidth_; j++) { |
| 1693 |
//pyzCount_[j] = 0; |
| 1694 |
pzzHist_[j] = 0.0; |
| 1695 |
} |
| 1696 |
// reset the counter |
| 1697 |
|
| 1698 |
Numcount_++; |
| 1699 |
if (Numcount_ > int(runTime_/statusTime_)) |
| 1700 |
cerr << "time =" << time << " Asum =" << Asum_ << '\n'; |
| 1701 |
if (Numcount_ > int(runTime_/statusTime_)) |
| 1702 |
cerr << "time =" << time << " Jsum =" << Jsum_ << '\n'; |
| 1703 |
|
| 1704 |
logFrameCount_ = 0; |
| 1705 |
} |
| 1706 |
} |
| 1707 |
|
