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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, 234107 (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 <sstream> |
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#include <string> |
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|
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#include "rnemd/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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#include "brains/Thermo.hpp" |
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#include "math/ConvexHull.hpp" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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#ifdef _MSC_VER |
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#define isnan(x) _isnan((x)) |
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#define isinf(x) (!_finite(x) && !_isnan(x)) |
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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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evaluatorA_(info), seleManA_(info), |
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commonA_(info), evaluatorB_(info), |
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seleManB_(info), commonB_(info), |
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usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { |
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|
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trialCount_ = 0; |
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failTrialCount_ = 0; |
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failRootCount_ = 0; |
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|
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Globals* simParams = info->getSimParams(); |
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RNEMDParameters* rnemdParams = simParams->getRNEMDParameters(); |
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|
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doRNEMD_ = rnemdParams->getUseRNEMD(); |
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if (!doRNEMD_) return; |
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|
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stringToMethod_["Swap"] = rnemdSwap; |
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stringToMethod_["NIVS"] = rnemdNIVS; |
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stringToMethod_["VSS"] = rnemdVSS; |
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|
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stringToFluxType_["KE"] = rnemdKE; |
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stringToFluxType_["Px"] = rnemdPx; |
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stringToFluxType_["Py"] = rnemdPy; |
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stringToFluxType_["Pz"] = rnemdPz; |
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stringToFluxType_["Pvector"] = rnemdPvector; |
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stringToFluxType_["Lx"] = rnemdLx; |
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stringToFluxType_["Ly"] = rnemdLy; |
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stringToFluxType_["Lz"] = rnemdLz; |
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stringToFluxType_["Lvector"] = rnemdLvector; |
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stringToFluxType_["KE+Px"] = rnemdKePx; |
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stringToFluxType_["KE+Py"] = rnemdKePy; |
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stringToFluxType_["KE+Pvector"] = rnemdKePvector; |
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stringToFluxType_["KE+Lx"] = rnemdKeLx; |
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stringToFluxType_["KE+Ly"] = rnemdKeLy; |
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stringToFluxType_["KE+Lz"] = rnemdKeLz; |
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stringToFluxType_["KE+Lvector"] = rnemdKeLvector; |
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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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const string methStr = rnemdParams->getMethod(); |
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bool hasFluxType = rnemdParams->haveFluxType(); |
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|
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rnemdObjectSelection_ = rnemdParams->getObjectSelection(); |
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|
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string fluxStr; |
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if (hasFluxType) { |
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fluxStr = rnemdParams->getFluxType(); |
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} else { |
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sprintf(painCave.errMsg, |
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"RNEMD: No fluxType was set in the md file. This parameter,\n" |
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"\twhich must be one of the following values:\n" |
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"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n" |
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"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n" |
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"\tmust be set to use RNEMD\n"); |
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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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bool hasKineticFlux = rnemdParams->haveKineticFlux(); |
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bool hasMomentumFlux = rnemdParams->haveMomentumFlux(); |
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bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector(); |
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bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux(); |
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bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector(); |
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hasSelectionA_ = rnemdParams->haveSelectionA(); |
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hasSelectionB_ = rnemdParams->haveSelectionB(); |
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bool hasSlabWidth = rnemdParams->haveSlabWidth(); |
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bool hasSlabACenter = rnemdParams->haveSlabACenter(); |
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bool hasSlabBCenter = rnemdParams->haveSlabBCenter(); |
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bool hasSphereARadius = rnemdParams->haveSphereARadius(); |
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hasSphereBRadius_ = rnemdParams->haveSphereBRadius(); |
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bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin(); |
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bool hasOutputFileName = rnemdParams->haveOutputFileName(); |
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bool hasOutputFields = rnemdParams->haveOutputFields(); |
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|
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map<string, RNEMDMethod>::iterator i; |
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i = stringToMethod_.find(methStr); |
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if (i != stringToMethod_.end()) |
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rnemdMethod_ = i->second; |
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else { |
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sprintf(painCave.errMsg, |
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"RNEMD: The current method,\n" |
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"\t\t%s is not one of the recognized\n" |
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"\texchange methods: Swap, NIVS, or VSS\n", |
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methStr.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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map<string, RNEMDFluxType>::iterator j; |
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j = stringToFluxType_.find(fluxStr); |
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if (j != stringToFluxType_.end()) |
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rnemdFluxType_ = j->second; |
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else { |
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sprintf(painCave.errMsg, |
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"RNEMD: The current fluxType,\n" |
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"\t\t%s\n" |
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"\tis not one of the recognized flux types.\n", |
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fluxStr.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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bool methodFluxMismatch = false; |
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bool hasCorrectFlux = false; |
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switch(rnemdMethod_) { |
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case rnemdSwap: |
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switch (rnemdFluxType_) { |
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case rnemdKE: |
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hasCorrectFlux = hasKineticFlux; |
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break; |
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case rnemdPx: |
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case rnemdPy: |
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case rnemdPz: |
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hasCorrectFlux = hasMomentumFlux; |
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break; |
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default : |
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methodFluxMismatch = true; |
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break; |
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} |
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break; |
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case rnemdNIVS: |
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switch (rnemdFluxType_) { |
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case rnemdKE: |
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case rnemdRotKE: |
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case rnemdFullKE: |
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hasCorrectFlux = hasKineticFlux; |
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break; |
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case rnemdPx: |
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case rnemdPy: |
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case rnemdPz: |
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hasCorrectFlux = hasMomentumFlux; |
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break; |
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case rnemdKePx: |
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case rnemdKePy: |
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hasCorrectFlux = hasMomentumFlux && hasKineticFlux; |
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break; |
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default: |
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methodFluxMismatch = true; |
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break; |
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} |
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break; |
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case rnemdVSS: |
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switch (rnemdFluxType_) { |
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case rnemdKE: |
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case rnemdRotKE: |
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case rnemdFullKE: |
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hasCorrectFlux = hasKineticFlux; |
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break; |
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case rnemdPx: |
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case rnemdPy: |
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case rnemdPz: |
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hasCorrectFlux = hasMomentumFlux; |
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break; |
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case rnemdLx: |
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case rnemdLy: |
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case rnemdLz: |
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hasCorrectFlux = hasAngularMomentumFlux; |
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break; |
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case rnemdPvector: |
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hasCorrectFlux = hasMomentumFluxVector; |
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break; |
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case rnemdLvector: |
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hasCorrectFlux = hasAngularMomentumFluxVector; |
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break; |
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case rnemdKePx: |
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case rnemdKePy: |
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hasCorrectFlux = hasMomentumFlux && hasKineticFlux; |
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break; |
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case rnemdKeLx: |
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case rnemdKeLy: |
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case rnemdKeLz: |
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hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux; |
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break; |
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case rnemdKePvector: |
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hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux; |
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break; |
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case rnemdKeLvector: |
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hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux; |
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break; |
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default: |
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methodFluxMismatch = true; |
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break; |
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} |
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default: |
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break; |
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} |
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|
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if (methodFluxMismatch) { |
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sprintf(painCave.errMsg, |
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"RNEMD: The current method,\n" |
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"\t\t%s\n" |
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"\tcannot be used with the current flux type, %s\n", |
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methStr.c_str(), fluxStr.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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if (!hasCorrectFlux) { |
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sprintf(painCave.errMsg, |
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"RNEMD: The current method, %s, and flux type, %s,\n" |
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"\tdid not have the correct flux value specified. Options\n" |
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"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n" |
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"\tmomentumFluxVector, and angularMomentumFluxVector.\n", |
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methStr.c_str(), fluxStr.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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if (hasKineticFlux) { |
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// convert the kcal / mol / Angstroms^2 / fs values in the md file |
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// into amu / fs^3: |
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kineticFlux_ = rnemdParams->getKineticFlux() |
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* PhysicalConstants::energyConvert; |
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} else { |
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kineticFlux_ = 0.0; |
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} |
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if (hasMomentumFluxVector) { |
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momentumFluxVector_ = rnemdParams->getMomentumFluxVector(); |
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} else { |
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momentumFluxVector_ = V3Zero; |
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if (hasMomentumFlux) { |
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RealType momentumFlux = rnemdParams->getMomentumFlux(); |
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switch (rnemdFluxType_) { |
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case rnemdPx: |
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momentumFluxVector_.x() = momentumFlux; |
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break; |
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case rnemdPy: |
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momentumFluxVector_.y() = momentumFlux; |
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break; |
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case rnemdPz: |
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momentumFluxVector_.z() = momentumFlux; |
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break; |
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case rnemdKePx: |
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momentumFluxVector_.x() = momentumFlux; |
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break; |
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case rnemdKePy: |
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momentumFluxVector_.y() = momentumFlux; |
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break; |
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default: |
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break; |
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} |
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} |
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if (hasAngularMomentumFluxVector) { |
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angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector(); |
| 320 |
} else { |
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angularMomentumFluxVector_ = V3Zero; |
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if (hasAngularMomentumFlux) { |
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RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux(); |
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switch (rnemdFluxType_) { |
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case rnemdLx: |
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angularMomentumFluxVector_.x() = angularMomentumFlux; |
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break; |
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case rnemdLy: |
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angularMomentumFluxVector_.y() = angularMomentumFlux; |
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break; |
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case rnemdLz: |
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angularMomentumFluxVector_.z() = angularMomentumFlux; |
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break; |
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case rnemdKeLx: |
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angularMomentumFluxVector_.x() = angularMomentumFlux; |
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break; |
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case rnemdKeLy: |
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angularMomentumFluxVector_.y() = angularMomentumFlux; |
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break; |
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case rnemdKeLz: |
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angularMomentumFluxVector_.z() = angularMomentumFlux; |
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break; |
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default: |
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break; |
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} |
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} |
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} |
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|
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if (hasCoordinateOrigin) { |
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coordinateOrigin_ = rnemdParams->getCoordinateOrigin(); |
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} else { |
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coordinateOrigin_ = V3Zero; |
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} |
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|
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// do some sanity checking |
| 356 |
|
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int selectionCount = seleMan_.getSelectionCount(); |
| 358 |
|
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int nIntegrable = info->getNGlobalIntegrableObjects(); |
| 360 |
|
| 361 |
if (selectionCount > nIntegrable) { |
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sprintf(painCave.errMsg, |
| 363 |
"RNEMD: The current objectSelection,\n" |
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"\t\t%s\n" |
| 365 |
"\thas resulted in %d selected objects. However,\n" |
| 366 |
"\tthe total number of integrable objects in the system\n" |
| 367 |
"\tis only %d. This is almost certainly not what you want\n" |
| 368 |
"\tto do. A likely cause of this is forgetting the _RB_0\n" |
| 369 |
"\tselector in the selection script!\n", |
| 370 |
rnemdObjectSelection_.c_str(), |
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selectionCount, nIntegrable); |
| 372 |
painCave.isFatal = 0; |
| 373 |
painCave.severity = OPENMD_WARNING; |
| 374 |
simError(); |
| 375 |
} |
| 376 |
|
| 377 |
areaAccumulator_ = new Accumulator(); |
| 378 |
|
| 379 |
nBins_ = rnemdParams->getOutputBins(); |
| 380 |
binWidth_ = rnemdParams->getOutputBinWidth(); |
| 381 |
|
| 382 |
data_.resize(RNEMD::ENDINDEX); |
| 383 |
OutputData z; |
| 384 |
z.units = "Angstroms"; |
| 385 |
z.title = "Z"; |
| 386 |
z.dataType = "RealType"; |
| 387 |
z.accumulator.reserve(nBins_); |
| 388 |
for (int i = 0; i < nBins_; i++) |
| 389 |
z.accumulator.push_back( new Accumulator() ); |
| 390 |
data_[Z] = z; |
| 391 |
outputMap_["Z"] = Z; |
| 392 |
|
| 393 |
OutputData r; |
| 394 |
r.units = "Angstroms"; |
| 395 |
r.title = "R"; |
| 396 |
r.dataType = "RealType"; |
| 397 |
r.accumulator.reserve(nBins_); |
| 398 |
for (int i = 0; i < nBins_; i++) |
| 399 |
r.accumulator.push_back( new Accumulator() ); |
| 400 |
data_[R] = r; |
| 401 |
outputMap_["R"] = R; |
| 402 |
|
| 403 |
OutputData temperature; |
| 404 |
temperature.units = "K"; |
| 405 |
temperature.title = "Temperature"; |
| 406 |
temperature.dataType = "RealType"; |
| 407 |
temperature.accumulator.reserve(nBins_); |
| 408 |
for (int i = 0; i < nBins_; i++) |
| 409 |
temperature.accumulator.push_back( new Accumulator() ); |
| 410 |
data_[TEMPERATURE] = temperature; |
| 411 |
outputMap_["TEMPERATURE"] = TEMPERATURE; |
| 412 |
|
| 413 |
OutputData velocity; |
| 414 |
velocity.units = "angstroms/fs"; |
| 415 |
velocity.title = "Velocity"; |
| 416 |
velocity.dataType = "Vector3d"; |
| 417 |
velocity.accumulator.reserve(nBins_); |
| 418 |
for (int i = 0; i < nBins_; i++) |
| 419 |
velocity.accumulator.push_back( new VectorAccumulator() ); |
| 420 |
data_[VELOCITY] = velocity; |
| 421 |
outputMap_["VELOCITY"] = VELOCITY; |
| 422 |
|
| 423 |
OutputData density; |
| 424 |
density.units = "g cm^-3"; |
| 425 |
density.title = "Density"; |
| 426 |
density.dataType = "RealType"; |
| 427 |
density.accumulator.reserve(nBins_); |
| 428 |
for (int i = 0; i < nBins_; i++) |
| 429 |
density.accumulator.push_back( new Accumulator() ); |
| 430 |
data_[DENSITY] = density; |
| 431 |
outputMap_["DENSITY"] = DENSITY; |
| 432 |
|
| 433 |
if (hasOutputFields) { |
| 434 |
parseOutputFileFormat(rnemdParams->getOutputFields()); |
| 435 |
} else { |
| 436 |
if (usePeriodicBoundaryConditions_) |
| 437 |
outputMask_.set(Z); |
| 438 |
else |
| 439 |
outputMask_.set(R); |
| 440 |
switch (rnemdFluxType_) { |
| 441 |
case rnemdKE: |
| 442 |
case rnemdRotKE: |
| 443 |
case rnemdFullKE: |
| 444 |
outputMask_.set(TEMPERATURE); |
| 445 |
break; |
| 446 |
case rnemdPx: |
| 447 |
case rnemdPy: |
| 448 |
outputMask_.set(VELOCITY); |
| 449 |
break; |
| 450 |
case rnemdPz: |
| 451 |
case rnemdPvector: |
| 452 |
outputMask_.set(VELOCITY); |
| 453 |
outputMask_.set(DENSITY); |
| 454 |
break; |
| 455 |
case rnemdLx: |
| 456 |
case rnemdLy: |
| 457 |
case rnemdLz: |
| 458 |
case rnemdLvector: |
| 459 |
outputMask_.set(ANGULARVELOCITY); |
| 460 |
break; |
| 461 |
case rnemdKeLx: |
| 462 |
case rnemdKeLy: |
| 463 |
case rnemdKeLz: |
| 464 |
case rnemdKeLvector: |
| 465 |
outputMask_.set(TEMPERATURE); |
| 466 |
outputMask_.set(ANGULARVELOCITY); |
| 467 |
break; |
| 468 |
case rnemdKePx: |
| 469 |
case rnemdKePy: |
| 470 |
outputMask_.set(TEMPERATURE); |
| 471 |
outputMask_.set(VELOCITY); |
| 472 |
break; |
| 473 |
case rnemdKePvector: |
| 474 |
outputMask_.set(TEMPERATURE); |
| 475 |
outputMask_.set(VELOCITY); |
| 476 |
outputMask_.set(DENSITY); |
| 477 |
break; |
| 478 |
default: |
| 479 |
break; |
| 480 |
} |
| 481 |
} |
| 482 |
|
| 483 |
if (hasOutputFileName) { |
| 484 |
rnemdFileName_ = rnemdParams->getOutputFileName(); |
| 485 |
} else { |
| 486 |
rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd"; |
| 487 |
} |
| 488 |
|
| 489 |
exchangeTime_ = rnemdParams->getExchangeTime(); |
| 490 |
|
| 491 |
Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot(); |
| 492 |
// total exchange sums are zeroed out at the beginning: |
| 493 |
|
| 494 |
kineticExchange_ = 0.0; |
| 495 |
momentumExchange_ = V3Zero; |
| 496 |
angularMomentumExchange_ = V3Zero; |
| 497 |
|
| 498 |
std::ostringstream selectionAstream; |
| 499 |
std::ostringstream selectionBstream; |
| 500 |
|
| 501 |
if (hasSelectionA_) { |
| 502 |
selectionA_ = rnemdParams->getSelectionA(); |
| 503 |
} else { |
| 504 |
if (usePeriodicBoundaryConditions_) { |
| 505 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 506 |
|
| 507 |
if (hasSlabWidth) |
| 508 |
slabWidth_ = rnemdParams->getSlabWidth(); |
| 509 |
else |
| 510 |
slabWidth_ = hmat(2,2) / 10.0; |
| 511 |
|
| 512 |
if (hasSlabACenter) |
| 513 |
slabACenter_ = rnemdParams->getSlabACenter(); |
| 514 |
else |
| 515 |
slabACenter_ = 0.0; |
| 516 |
|
| 517 |
selectionAstream << "select wrappedz > " |
| 518 |
<< slabACenter_ - 0.5*slabWidth_ |
| 519 |
<< " && wrappedz < " |
| 520 |
<< slabACenter_ + 0.5*slabWidth_; |
| 521 |
selectionA_ = selectionAstream.str(); |
| 522 |
} else { |
| 523 |
if (hasSphereARadius) |
| 524 |
sphereARadius_ = rnemdParams->getSphereARadius(); |
| 525 |
else { |
| 526 |
// use an initial guess to the size of the inner slab to be 1/10 the |
| 527 |
// radius of an approximately spherical hull: |
| 528 |
Thermo thermo(info); |
| 529 |
RealType hVol = thermo.getHullVolume(); |
| 530 |
sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0); |
| 531 |
} |
| 532 |
selectionAstream << "select r < " << sphereARadius_; |
| 533 |
selectionA_ = selectionAstream.str(); |
| 534 |
} |
| 535 |
} |
| 536 |
|
| 537 |
if (hasSelectionB_) { |
| 538 |
selectionB_ = rnemdParams->getSelectionB(); |
| 539 |
} else { |
| 540 |
if (usePeriodicBoundaryConditions_) { |
| 541 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 542 |
|
| 543 |
if (hasSlabWidth) |
| 544 |
slabWidth_ = rnemdParams->getSlabWidth(); |
| 545 |
else |
| 546 |
slabWidth_ = hmat(2,2) / 10.0; |
| 547 |
|
| 548 |
if (hasSlabBCenter) |
| 549 |
slabBCenter_ = rnemdParams->getSlabACenter(); |
| 550 |
else |
| 551 |
slabBCenter_ = hmat(2,2) / 2.0; |
| 552 |
|
| 553 |
selectionBstream << "select wrappedz > " |
| 554 |
<< slabBCenter_ - 0.5*slabWidth_ |
| 555 |
<< " && wrappedz < " |
| 556 |
<< slabBCenter_ + 0.5*slabWidth_; |
| 557 |
selectionB_ = selectionBstream.str(); |
| 558 |
} else { |
| 559 |
if (hasSphereBRadius_) { |
| 560 |
sphereBRadius_ = rnemdParams->getSphereBRadius(); |
| 561 |
selectionBstream << "select r > " << sphereBRadius_; |
| 562 |
selectionB_ = selectionBstream.str(); |
| 563 |
} else { |
| 564 |
selectionB_ = "select hull"; |
| 565 |
hasSelectionB_ = true; |
| 566 |
} |
| 567 |
} |
| 568 |
} |
| 569 |
} |
| 570 |
// object evaluator: |
| 571 |
evaluator_.loadScriptString(rnemdObjectSelection_); |
| 572 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 573 |
|
| 574 |
evaluatorA_.loadScriptString(selectionA_); |
| 575 |
evaluatorB_.loadScriptString(selectionB_); |
| 576 |
|
| 577 |
seleManA_.setSelectionSet(evaluatorA_.evaluate()); |
| 578 |
seleManB_.setSelectionSet(evaluatorB_.evaluate()); |
| 579 |
|
| 580 |
commonA_ = seleManA_ & seleMan_; |
| 581 |
commonB_ = seleManB_ & seleMan_; |
| 582 |
} |
| 583 |
|
| 584 |
|
| 585 |
RNEMD::~RNEMD() { |
| 586 |
if (!doRNEMD_) return; |
| 587 |
#ifdef IS_MPI |
| 588 |
if (worldRank == 0) { |
| 589 |
#endif |
| 590 |
|
| 591 |
writeOutputFile(); |
| 592 |
|
| 593 |
rnemdFile_.close(); |
| 594 |
|
| 595 |
#ifdef IS_MPI |
| 596 |
} |
| 597 |
#endif |
| 598 |
} |
| 599 |
|
| 600 |
void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) { |
| 601 |
if (!doRNEMD_) return; |
| 602 |
int selei; |
| 603 |
int selej; |
| 604 |
|
| 605 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 606 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 607 |
|
| 608 |
StuntDouble* sd; |
| 609 |
|
| 610 |
RealType min_val; |
| 611 |
bool min_found = false; |
| 612 |
StuntDouble* min_sd; |
| 613 |
|
| 614 |
RealType max_val; |
| 615 |
bool max_found = false; |
| 616 |
StuntDouble* max_sd; |
| 617 |
|
| 618 |
for (sd = seleManA_.beginSelected(selei); sd != NULL; |
| 619 |
sd = seleManA_.nextSelected(selei)) { |
| 620 |
|
| 621 |
Vector3d pos = sd->getPos(); |
| 622 |
|
| 623 |
// wrap the stuntdouble's position back into the box: |
| 624 |
|
| 625 |
if (usePeriodicBoundaryConditions_) |
| 626 |
currentSnap_->wrapVector(pos); |
| 627 |
|
| 628 |
RealType mass = sd->getMass(); |
| 629 |
Vector3d vel = sd->getVel(); |
| 630 |
RealType value; |
| 631 |
|
| 632 |
switch(rnemdFluxType_) { |
| 633 |
case rnemdKE : |
| 634 |
|
| 635 |
value = mass * vel.lengthSquare(); |
| 636 |
|
| 637 |
if (sd->isDirectional()) { |
| 638 |
Vector3d angMom = sd->getJ(); |
| 639 |
Mat3x3d I = sd->getI(); |
| 640 |
|
| 641 |
if (sd->isLinear()) { |
| 642 |
int i = sd->linearAxis(); |
| 643 |
int j = (i + 1) % 3; |
| 644 |
int k = (i + 2) % 3; |
| 645 |
value += angMom[j] * angMom[j] / I(j, j) + |
| 646 |
angMom[k] * angMom[k] / I(k, k); |
| 647 |
} else { |
| 648 |
value += angMom[0]*angMom[0]/I(0, 0) |
| 649 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 650 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 651 |
} |
| 652 |
} //angular momenta exchange enabled |
| 653 |
value *= 0.5; |
| 654 |
break; |
| 655 |
case rnemdPx : |
| 656 |
value = mass * vel[0]; |
| 657 |
break; |
| 658 |
case rnemdPy : |
| 659 |
value = mass * vel[1]; |
| 660 |
break; |
| 661 |
case rnemdPz : |
| 662 |
value = mass * vel[2]; |
| 663 |
break; |
| 664 |
default : |
| 665 |
break; |
| 666 |
} |
| 667 |
if (!max_found) { |
| 668 |
max_val = value; |
| 669 |
max_sd = sd; |
| 670 |
max_found = true; |
| 671 |
} else { |
| 672 |
if (max_val < value) { |
| 673 |
max_val = value; |
| 674 |
max_sd = sd; |
| 675 |
} |
| 676 |
} |
| 677 |
} |
| 678 |
|
| 679 |
for (sd = seleManB_.beginSelected(selej); sd != NULL; |
| 680 |
sd = seleManB_.nextSelected(selej)) { |
| 681 |
|
| 682 |
Vector3d pos = sd->getPos(); |
| 683 |
|
| 684 |
// wrap the stuntdouble's position back into the box: |
| 685 |
|
| 686 |
if (usePeriodicBoundaryConditions_) |
| 687 |
currentSnap_->wrapVector(pos); |
| 688 |
|
| 689 |
RealType mass = sd->getMass(); |
| 690 |
Vector3d vel = sd->getVel(); |
| 691 |
RealType value; |
| 692 |
|
| 693 |
switch(rnemdFluxType_) { |
| 694 |
case rnemdKE : |
| 695 |
|
| 696 |
value = mass * vel.lengthSquare(); |
| 697 |
|
| 698 |
if (sd->isDirectional()) { |
| 699 |
Vector3d angMom = sd->getJ(); |
| 700 |
Mat3x3d I = sd->getI(); |
| 701 |
|
| 702 |
if (sd->isLinear()) { |
| 703 |
int i = sd->linearAxis(); |
| 704 |
int j = (i + 1) % 3; |
| 705 |
int k = (i + 2) % 3; |
| 706 |
value += angMom[j] * angMom[j] / I(j, j) + |
| 707 |
angMom[k] * angMom[k] / I(k, k); |
| 708 |
} else { |
| 709 |
value += angMom[0]*angMom[0]/I(0, 0) |
| 710 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 711 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 712 |
} |
| 713 |
} //angular momenta exchange enabled |
| 714 |
value *= 0.5; |
| 715 |
break; |
| 716 |
case rnemdPx : |
| 717 |
value = mass * vel[0]; |
| 718 |
break; |
| 719 |
case rnemdPy : |
| 720 |
value = mass * vel[1]; |
| 721 |
break; |
| 722 |
case rnemdPz : |
| 723 |
value = mass * vel[2]; |
| 724 |
break; |
| 725 |
default : |
| 726 |
break; |
| 727 |
} |
| 728 |
|
| 729 |
if (!min_found) { |
| 730 |
min_val = value; |
| 731 |
min_sd = sd; |
| 732 |
min_found = true; |
| 733 |
} else { |
| 734 |
if (min_val > value) { |
| 735 |
min_val = value; |
| 736 |
min_sd = sd; |
| 737 |
} |
| 738 |
} |
| 739 |
} |
| 740 |
|
| 741 |
#ifdef IS_MPI |
| 742 |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 743 |
|
| 744 |
bool my_min_found = min_found; |
| 745 |
bool my_max_found = max_found; |
| 746 |
|
| 747 |
// Even if we didn't find a minimum, did someone else? |
| 748 |
MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR); |
| 749 |
// Even if we didn't find a maximum, did someone else? |
| 750 |
MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR); |
| 751 |
#endif |
| 752 |
|
| 753 |
if (max_found && min_found) { |
| 754 |
|
| 755 |
#ifdef IS_MPI |
| 756 |
struct { |
| 757 |
RealType val; |
| 758 |
int rank; |
| 759 |
} max_vals, min_vals; |
| 760 |
|
| 761 |
if (my_min_found) { |
| 762 |
min_vals.val = min_val; |
| 763 |
} else { |
| 764 |
min_vals.val = HONKING_LARGE_VALUE; |
| 765 |
} |
| 766 |
min_vals.rank = worldRank; |
| 767 |
|
| 768 |
// Who had the minimum? |
| 769 |
MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals, |
| 770 |
1, MPI::REALTYPE_INT, MPI::MINLOC); |
| 771 |
min_val = min_vals.val; |
| 772 |
|
| 773 |
if (my_max_found) { |
| 774 |
max_vals.val = max_val; |
| 775 |
} else { |
| 776 |
max_vals.val = -HONKING_LARGE_VALUE; |
| 777 |
} |
| 778 |
max_vals.rank = worldRank; |
| 779 |
|
| 780 |
// Who had the maximum? |
| 781 |
MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals, |
| 782 |
1, MPI::REALTYPE_INT, MPI::MAXLOC); |
| 783 |
max_val = max_vals.val; |
| 784 |
#endif |
| 785 |
|
| 786 |
if (min_val < max_val) { |
| 787 |
|
| 788 |
#ifdef IS_MPI |
| 789 |
if (max_vals.rank == worldRank && min_vals.rank == worldRank) { |
| 790 |
// I have both maximum and minimum, so proceed like a single |
| 791 |
// processor version: |
| 792 |
#endif |
| 793 |
|
| 794 |
Vector3d min_vel = min_sd->getVel(); |
| 795 |
Vector3d max_vel = max_sd->getVel(); |
| 796 |
RealType temp_vel; |
| 797 |
|
| 798 |
switch(rnemdFluxType_) { |
| 799 |
case rnemdKE : |
| 800 |
min_sd->setVel(max_vel); |
| 801 |
max_sd->setVel(min_vel); |
| 802 |
if (min_sd->isDirectional() && max_sd->isDirectional()) { |
| 803 |
Vector3d min_angMom = min_sd->getJ(); |
| 804 |
Vector3d max_angMom = max_sd->getJ(); |
| 805 |
min_sd->setJ(max_angMom); |
| 806 |
max_sd->setJ(min_angMom); |
| 807 |
}//angular momenta exchange enabled |
| 808 |
//assumes same rigid body identity |
| 809 |
break; |
| 810 |
case rnemdPx : |
| 811 |
temp_vel = min_vel.x(); |
| 812 |
min_vel.x() = max_vel.x(); |
| 813 |
max_vel.x() = temp_vel; |
| 814 |
min_sd->setVel(min_vel); |
| 815 |
max_sd->setVel(max_vel); |
| 816 |
break; |
| 817 |
case rnemdPy : |
| 818 |
temp_vel = min_vel.y(); |
| 819 |
min_vel.y() = max_vel.y(); |
| 820 |
max_vel.y() = temp_vel; |
| 821 |
min_sd->setVel(min_vel); |
| 822 |
max_sd->setVel(max_vel); |
| 823 |
break; |
| 824 |
case rnemdPz : |
| 825 |
temp_vel = min_vel.z(); |
| 826 |
min_vel.z() = max_vel.z(); |
| 827 |
max_vel.z() = temp_vel; |
| 828 |
min_sd->setVel(min_vel); |
| 829 |
max_sd->setVel(max_vel); |
| 830 |
break; |
| 831 |
default : |
| 832 |
break; |
| 833 |
} |
| 834 |
|
| 835 |
#ifdef IS_MPI |
| 836 |
// the rest of the cases only apply in parallel simulations: |
| 837 |
} else if (max_vals.rank == worldRank) { |
| 838 |
// I had the max, but not the minimum |
| 839 |
|
| 840 |
Vector3d min_vel; |
| 841 |
Vector3d max_vel = max_sd->getVel(); |
| 842 |
MPI::Status status; |
| 843 |
|
| 844 |
// point-to-point swap of the velocity vector |
| 845 |
MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 846 |
min_vals.rank, 0, |
| 847 |
min_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 848 |
min_vals.rank, 0, status); |
| 849 |
|
| 850 |
switch(rnemdFluxType_) { |
| 851 |
case rnemdKE : |
| 852 |
max_sd->setVel(min_vel); |
| 853 |
//angular momenta exchange enabled |
| 854 |
if (max_sd->isDirectional()) { |
| 855 |
Vector3d min_angMom; |
| 856 |
Vector3d max_angMom = max_sd->getJ(); |
| 857 |
|
| 858 |
// point-to-point swap of the angular momentum vector |
| 859 |
MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3, |
| 860 |
MPI::REALTYPE, min_vals.rank, 1, |
| 861 |
min_angMom.getArrayPointer(), 3, |
| 862 |
MPI::REALTYPE, min_vals.rank, 1, |
| 863 |
status); |
| 864 |
|
| 865 |
max_sd->setJ(min_angMom); |
| 866 |
} |
| 867 |
break; |
| 868 |
case rnemdPx : |
| 869 |
max_vel.x() = min_vel.x(); |
| 870 |
max_sd->setVel(max_vel); |
| 871 |
break; |
| 872 |
case rnemdPy : |
| 873 |
max_vel.y() = min_vel.y(); |
| 874 |
max_sd->setVel(max_vel); |
| 875 |
break; |
| 876 |
case rnemdPz : |
| 877 |
max_vel.z() = min_vel.z(); |
| 878 |
max_sd->setVel(max_vel); |
| 879 |
break; |
| 880 |
default : |
| 881 |
break; |
| 882 |
} |
| 883 |
} else if (min_vals.rank == worldRank) { |
| 884 |
// I had the minimum but not the maximum: |
| 885 |
|
| 886 |
Vector3d max_vel; |
| 887 |
Vector3d min_vel = min_sd->getVel(); |
| 888 |
MPI::Status status; |
| 889 |
|
| 890 |
// point-to-point swap of the velocity vector |
| 891 |
MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 892 |
max_vals.rank, 0, |
| 893 |
max_vel.getArrayPointer(), 3, MPI::REALTYPE, |
| 894 |
max_vals.rank, 0, status); |
| 895 |
|
| 896 |
switch(rnemdFluxType_) { |
| 897 |
case rnemdKE : |
| 898 |
min_sd->setVel(max_vel); |
| 899 |
//angular momenta exchange enabled |
| 900 |
if (min_sd->isDirectional()) { |
| 901 |
Vector3d min_angMom = min_sd->getJ(); |
| 902 |
Vector3d max_angMom; |
| 903 |
|
| 904 |
// point-to-point swap of the angular momentum vector |
| 905 |
MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3, |
| 906 |
MPI::REALTYPE, max_vals.rank, 1, |
| 907 |
max_angMom.getArrayPointer(), 3, |
| 908 |
MPI::REALTYPE, max_vals.rank, 1, |
| 909 |
status); |
| 910 |
|
| 911 |
min_sd->setJ(max_angMom); |
| 912 |
} |
| 913 |
break; |
| 914 |
case rnemdPx : |
| 915 |
min_vel.x() = max_vel.x(); |
| 916 |
min_sd->setVel(min_vel); |
| 917 |
break; |
| 918 |
case rnemdPy : |
| 919 |
min_vel.y() = max_vel.y(); |
| 920 |
min_sd->setVel(min_vel); |
| 921 |
break; |
| 922 |
case rnemdPz : |
| 923 |
min_vel.z() = max_vel.z(); |
| 924 |
min_sd->setVel(min_vel); |
| 925 |
break; |
| 926 |
default : |
| 927 |
break; |
| 928 |
} |
| 929 |
} |
| 930 |
#endif |
| 931 |
|
| 932 |
switch(rnemdFluxType_) { |
| 933 |
case rnemdKE: |
| 934 |
kineticExchange_ += max_val - min_val; |
| 935 |
break; |
| 936 |
case rnemdPx: |
| 937 |
momentumExchange_.x() += max_val - min_val; |
| 938 |
break; |
| 939 |
case rnemdPy: |
| 940 |
momentumExchange_.y() += max_val - min_val; |
| 941 |
break; |
| 942 |
case rnemdPz: |
| 943 |
momentumExchange_.z() += max_val - min_val; |
| 944 |
break; |
| 945 |
default: |
| 946 |
break; |
| 947 |
} |
| 948 |
} else { |
| 949 |
sprintf(painCave.errMsg, |
| 950 |
"RNEMD::doSwap exchange NOT performed because min_val > max_val\n"); |
| 951 |
painCave.isFatal = 0; |
| 952 |
painCave.severity = OPENMD_INFO; |
| 953 |
simError(); |
| 954 |
failTrialCount_++; |
| 955 |
} |
| 956 |
} else { |
| 957 |
sprintf(painCave.errMsg, |
| 958 |
"RNEMD::doSwap exchange NOT performed because selected object\n" |
| 959 |
"\twas not present in at least one of the two slabs.\n"); |
| 960 |
painCave.isFatal = 0; |
| 961 |
painCave.severity = OPENMD_INFO; |
| 962 |
simError(); |
| 963 |
failTrialCount_++; |
| 964 |
} |
| 965 |
} |
| 966 |
|
| 967 |
void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) { |
| 968 |
if (!doRNEMD_) return; |
| 969 |
int selei; |
| 970 |
int selej; |
| 971 |
|
| 972 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 973 |
RealType time = currentSnap_->getTime(); |
| 974 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 975 |
|
| 976 |
StuntDouble* sd; |
| 977 |
|
| 978 |
vector<StuntDouble*> hotBin, coldBin; |
| 979 |
|
| 980 |
RealType Phx = 0.0; |
| 981 |
RealType Phy = 0.0; |
| 982 |
RealType Phz = 0.0; |
| 983 |
RealType Khx = 0.0; |
| 984 |
RealType Khy = 0.0; |
| 985 |
RealType Khz = 0.0; |
| 986 |
RealType Khw = 0.0; |
| 987 |
RealType Pcx = 0.0; |
| 988 |
RealType Pcy = 0.0; |
| 989 |
RealType Pcz = 0.0; |
| 990 |
RealType Kcx = 0.0; |
| 991 |
RealType Kcy = 0.0; |
| 992 |
RealType Kcz = 0.0; |
| 993 |
RealType Kcw = 0.0; |
| 994 |
|
| 995 |
for (sd = smanA.beginSelected(selei); sd != NULL; |
| 996 |
sd = smanA.nextSelected(selei)) { |
| 997 |
|
| 998 |
Vector3d pos = sd->getPos(); |
| 999 |
|
| 1000 |
// wrap the stuntdouble's position back into the box: |
| 1001 |
|
| 1002 |
if (usePeriodicBoundaryConditions_) |
| 1003 |
currentSnap_->wrapVector(pos); |
| 1004 |
|
| 1005 |
|
| 1006 |
RealType mass = sd->getMass(); |
| 1007 |
Vector3d vel = sd->getVel(); |
| 1008 |
|
| 1009 |
hotBin.push_back(sd); |
| 1010 |
Phx += mass * vel.x(); |
| 1011 |
Phy += mass * vel.y(); |
| 1012 |
Phz += mass * vel.z(); |
| 1013 |
Khx += mass * vel.x() * vel.x(); |
| 1014 |
Khy += mass * vel.y() * vel.y(); |
| 1015 |
Khz += mass * vel.z() * vel.z(); |
| 1016 |
if (sd->isDirectional()) { |
| 1017 |
Vector3d angMom = sd->getJ(); |
| 1018 |
Mat3x3d I = sd->getI(); |
| 1019 |
if (sd->isLinear()) { |
| 1020 |
int i = sd->linearAxis(); |
| 1021 |
int j = (i + 1) % 3; |
| 1022 |
int k = (i + 2) % 3; |
| 1023 |
Khw += angMom[j] * angMom[j] / I(j, j) + |
| 1024 |
angMom[k] * angMom[k] / I(k, k); |
| 1025 |
} else { |
| 1026 |
Khw += angMom[0]*angMom[0]/I(0, 0) |
| 1027 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 1028 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 1029 |
} |
| 1030 |
} |
| 1031 |
} |
| 1032 |
for (sd = smanB.beginSelected(selej); sd != NULL; |
| 1033 |
sd = smanB.nextSelected(selej)) { |
| 1034 |
Vector3d pos = sd->getPos(); |
| 1035 |
|
| 1036 |
// wrap the stuntdouble's position back into the box: |
| 1037 |
|
| 1038 |
if (usePeriodicBoundaryConditions_) |
| 1039 |
currentSnap_->wrapVector(pos); |
| 1040 |
|
| 1041 |
RealType mass = sd->getMass(); |
| 1042 |
Vector3d vel = sd->getVel(); |
| 1043 |
|
| 1044 |
coldBin.push_back(sd); |
| 1045 |
Pcx += mass * vel.x(); |
| 1046 |
Pcy += mass * vel.y(); |
| 1047 |
Pcz += mass * vel.z(); |
| 1048 |
Kcx += mass * vel.x() * vel.x(); |
| 1049 |
Kcy += mass * vel.y() * vel.y(); |
| 1050 |
Kcz += mass * vel.z() * vel.z(); |
| 1051 |
if (sd->isDirectional()) { |
| 1052 |
Vector3d angMom = sd->getJ(); |
| 1053 |
Mat3x3d I = sd->getI(); |
| 1054 |
if (sd->isLinear()) { |
| 1055 |
int i = sd->linearAxis(); |
| 1056 |
int j = (i + 1) % 3; |
| 1057 |
int k = (i + 2) % 3; |
| 1058 |
Kcw += angMom[j] * angMom[j] / I(j, j) + |
| 1059 |
angMom[k] * angMom[k] / I(k, k); |
| 1060 |
} else { |
| 1061 |
Kcw += angMom[0]*angMom[0]/I(0, 0) |
| 1062 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 1063 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 1064 |
} |
| 1065 |
} |
| 1066 |
} |
| 1067 |
|
| 1068 |
Khx *= 0.5; |
| 1069 |
Khy *= 0.5; |
| 1070 |
Khz *= 0.5; |
| 1071 |
Khw *= 0.5; |
| 1072 |
Kcx *= 0.5; |
| 1073 |
Kcy *= 0.5; |
| 1074 |
Kcz *= 0.5; |
| 1075 |
Kcw *= 0.5; |
| 1076 |
|
| 1077 |
#ifdef IS_MPI |
| 1078 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM); |
| 1079 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM); |
| 1080 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM); |
| 1081 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM); |
| 1082 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM); |
| 1083 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM); |
| 1084 |
|
| 1085 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM); |
| 1086 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM); |
| 1087 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM); |
| 1088 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM); |
| 1089 |
|
| 1090 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM); |
| 1091 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM); |
| 1092 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM); |
| 1093 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM); |
| 1094 |
#endif |
| 1095 |
|
| 1096 |
//solve coldBin coeff's first |
| 1097 |
RealType px = Pcx / Phx; |
| 1098 |
RealType py = Pcy / Phy; |
| 1099 |
RealType pz = Pcz / Phz; |
| 1100 |
RealType c, x, y, z; |
| 1101 |
bool successfulScale = false; |
| 1102 |
if ((rnemdFluxType_ == rnemdFullKE) || |
| 1103 |
(rnemdFluxType_ == rnemdRotKE)) { |
| 1104 |
//may need sanity check Khw & Kcw > 0 |
| 1105 |
|
| 1106 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1107 |
c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw); |
| 1108 |
} else { |
| 1109 |
c = 1.0 - kineticTarget_ / Kcw; |
| 1110 |
} |
| 1111 |
|
| 1112 |
if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients |
| 1113 |
c = sqrt(c); |
| 1114 |
|
| 1115 |
RealType w = 0.0; |
| 1116 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1117 |
x = 1.0 + px * (1.0 - c); |
| 1118 |
y = 1.0 + py * (1.0 - c); |
| 1119 |
z = 1.0 + pz * (1.0 - c); |
| 1120 |
/* more complicated way |
| 1121 |
w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz |
| 1122 |
+ Khx * px * px + Khy * py * py + Khz * pz * pz) |
| 1123 |
- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py) |
| 1124 |
+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px) |
| 1125 |
+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) |
| 1126 |
- Kcx - Kcy - Kcz)) / Khw; the following is simpler |
| 1127 |
*/ |
| 1128 |
if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) && |
| 1129 |
(fabs(z - 1.0) < 0.1)) { |
| 1130 |
w = 1.0 + (kineticTarget_ |
| 1131 |
+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y) |
| 1132 |
+ Khz * (1.0 - z * z)) / Khw; |
| 1133 |
}//no need to calculate w if x, y or z is out of range |
| 1134 |
} else { |
| 1135 |
w = 1.0 + kineticTarget_ / Khw; |
| 1136 |
} |
| 1137 |
if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients |
| 1138 |
//if w is in the right range, so should be x, y, z. |
| 1139 |
vector<StuntDouble*>::iterator sdi; |
| 1140 |
Vector3d vel; |
| 1141 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1142 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1143 |
vel = (*sdi)->getVel() * c; |
| 1144 |
(*sdi)->setVel(vel); |
| 1145 |
} |
| 1146 |
if ((*sdi)->isDirectional()) { |
| 1147 |
Vector3d angMom = (*sdi)->getJ() * c; |
| 1148 |
(*sdi)->setJ(angMom); |
| 1149 |
} |
| 1150 |
} |
| 1151 |
w = sqrt(w); |
| 1152 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1153 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1154 |
vel = (*sdi)->getVel(); |
| 1155 |
vel.x() *= x; |
| 1156 |
vel.y() *= y; |
| 1157 |
vel.z() *= z; |
| 1158 |
(*sdi)->setVel(vel); |
| 1159 |
} |
| 1160 |
if ((*sdi)->isDirectional()) { |
| 1161 |
Vector3d angMom = (*sdi)->getJ() * w; |
| 1162 |
(*sdi)->setJ(angMom); |
| 1163 |
} |
| 1164 |
} |
| 1165 |
successfulScale = true; |
| 1166 |
kineticExchange_ += kineticTarget_; |
| 1167 |
} |
| 1168 |
} |
| 1169 |
} else { |
| 1170 |
RealType a000, a110, c0, a001, a111, b01, b11, c1; |
| 1171 |
switch(rnemdFluxType_) { |
| 1172 |
case rnemdKE : |
| 1173 |
/* used hotBin coeff's & only scale x & y dimensions |
| 1174 |
RealType px = Phx / Pcx; |
| 1175 |
RealType py = Phy / Pcy; |
| 1176 |
a110 = Khy; |
| 1177 |
c0 = - Khx - Khy - kineticTarget_; |
| 1178 |
a000 = Khx; |
| 1179 |
a111 = Kcy * py * py; |
| 1180 |
b11 = -2.0 * Kcy * py * (1.0 + py); |
| 1181 |
c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_; |
| 1182 |
b01 = -2.0 * Kcx * px * (1.0 + px); |
| 1183 |
a001 = Kcx * px * px; |
| 1184 |
*/ |
| 1185 |
//scale all three dimensions, let c_x = c_y |
| 1186 |
a000 = Kcx + Kcy; |
| 1187 |
a110 = Kcz; |
| 1188 |
c0 = kineticTarget_ - Kcx - Kcy - Kcz; |
| 1189 |
a001 = Khx * px * px + Khy * py * py; |
| 1190 |
a111 = Khz * pz * pz; |
| 1191 |
b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)); |
| 1192 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 1193 |
c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) |
| 1194 |
+ Khz * pz * (2.0 + pz) - kineticTarget_; |
| 1195 |
break; |
| 1196 |
case rnemdPx : |
| 1197 |
c = 1 - momentumTarget_.x() / Pcx; |
| 1198 |
a000 = Kcy; |
| 1199 |
a110 = Kcz; |
| 1200 |
c0 = Kcx * c * c - Kcx - Kcy - Kcz; |
| 1201 |
a001 = py * py * Khy; |
| 1202 |
a111 = pz * pz * Khz; |
| 1203 |
b01 = -2.0 * Khy * py * (1.0 + py); |
| 1204 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 1205 |
c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz) |
| 1206 |
+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0); |
| 1207 |
break; |
| 1208 |
case rnemdPy : |
| 1209 |
c = 1 - momentumTarget_.y() / Pcy; |
| 1210 |
a000 = Kcx; |
| 1211 |
a110 = Kcz; |
| 1212 |
c0 = Kcy * c * c - Kcx - Kcy - Kcz; |
| 1213 |
a001 = px * px * Khx; |
| 1214 |
a111 = pz * pz * Khz; |
| 1215 |
b01 = -2.0 * Khx * px * (1.0 + px); |
| 1216 |
b11 = -2.0 * Khz * pz * (1.0 + pz); |
| 1217 |
c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz) |
| 1218 |
+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0); |
| 1219 |
break; |
| 1220 |
case rnemdPz ://we don't really do this, do we? |
| 1221 |
c = 1 - momentumTarget_.z() / Pcz; |
| 1222 |
a000 = Kcx; |
| 1223 |
a110 = Kcy; |
| 1224 |
c0 = Kcz * c * c - Kcx - Kcy - Kcz; |
| 1225 |
a001 = px * px * Khx; |
| 1226 |
a111 = py * py * Khy; |
| 1227 |
b01 = -2.0 * Khx * px * (1.0 + px); |
| 1228 |
b11 = -2.0 * Khy * py * (1.0 + py); |
| 1229 |
c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py) |
| 1230 |
+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0); |
| 1231 |
break; |
| 1232 |
default : |
| 1233 |
break; |
| 1234 |
} |
| 1235 |
|
| 1236 |
RealType v1 = a000 * a111 - a001 * a110; |
| 1237 |
RealType v2 = a000 * b01; |
| 1238 |
RealType v3 = a000 * b11; |
| 1239 |
RealType v4 = a000 * c1 - a001 * c0; |
| 1240 |
RealType v8 = a110 * b01; |
| 1241 |
RealType v10 = - b01 * c0; |
| 1242 |
|
| 1243 |
RealType u0 = v2 * v10 - v4 * v4; |
| 1244 |
RealType u1 = -2.0 * v3 * v4; |
| 1245 |
RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4; |
| 1246 |
RealType u3 = -2.0 * v1 * v3; |
| 1247 |
RealType u4 = - v1 * v1; |
| 1248 |
//rescale coefficients |
| 1249 |
RealType maxAbs = fabs(u0); |
| 1250 |
if (maxAbs < fabs(u1)) maxAbs = fabs(u1); |
| 1251 |
if (maxAbs < fabs(u2)) maxAbs = fabs(u2); |
| 1252 |
if (maxAbs < fabs(u3)) maxAbs = fabs(u3); |
| 1253 |
if (maxAbs < fabs(u4)) maxAbs = fabs(u4); |
| 1254 |
u0 /= maxAbs; |
| 1255 |
u1 /= maxAbs; |
| 1256 |
u2 /= maxAbs; |
| 1257 |
u3 /= maxAbs; |
| 1258 |
u4 /= maxAbs; |
| 1259 |
//max_element(start, end) is also available. |
| 1260 |
Polynomial<RealType> poly; //same as DoublePolynomial poly; |
| 1261 |
poly.setCoefficient(4, u4); |
| 1262 |
poly.setCoefficient(3, u3); |
| 1263 |
poly.setCoefficient(2, u2); |
| 1264 |
poly.setCoefficient(1, u1); |
| 1265 |
poly.setCoefficient(0, u0); |
| 1266 |
vector<RealType> realRoots = poly.FindRealRoots(); |
| 1267 |
|
| 1268 |
vector<RealType>::iterator ri; |
| 1269 |
RealType r1, r2, alpha0; |
| 1270 |
vector<pair<RealType,RealType> > rps; |
| 1271 |
for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) { |
| 1272 |
r2 = *ri; |
| 1273 |
//check if FindRealRoots() give the right answer |
| 1274 |
if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) { |
| 1275 |
sprintf(painCave.errMsg, |
| 1276 |
"RNEMD Warning: polynomial solve seems to have an error!"); |
| 1277 |
painCave.isFatal = 0; |
| 1278 |
simError(); |
| 1279 |
failRootCount_++; |
| 1280 |
} |
| 1281 |
//might not be useful w/o rescaling coefficients |
| 1282 |
alpha0 = -c0 - a110 * r2 * r2; |
| 1283 |
if (alpha0 >= 0.0) { |
| 1284 |
r1 = sqrt(alpha0 / a000); |
| 1285 |
if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) |
| 1286 |
< 1e-6) |
| 1287 |
{ rps.push_back(make_pair(r1, r2)); } |
| 1288 |
if (r1 > 1e-6) { //r1 non-negative |
| 1289 |
r1 = -r1; |
| 1290 |
if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111)) |
| 1291 |
< 1e-6) |
| 1292 |
{ rps.push_back(make_pair(r1, r2)); } |
| 1293 |
} |
| 1294 |
} |
| 1295 |
} |
| 1296 |
// Consider combining together the solving pair part w/ the searching |
| 1297 |
// best solution part so that we don't need the pairs vector |
| 1298 |
if (!rps.empty()) { |
| 1299 |
RealType smallestDiff = HONKING_LARGE_VALUE; |
| 1300 |
RealType diff; |
| 1301 |
pair<RealType,RealType> bestPair = make_pair(1.0, 1.0); |
| 1302 |
vector<pair<RealType,RealType> >::iterator rpi; |
| 1303 |
for (rpi = rps.begin(); rpi != rps.end(); rpi++) { |
| 1304 |
r1 = (*rpi).first; |
| 1305 |
r2 = (*rpi).second; |
| 1306 |
switch(rnemdFluxType_) { |
| 1307 |
case rnemdKE : |
| 1308 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1309 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2) |
| 1310 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); |
| 1311 |
break; |
| 1312 |
case rnemdPx : |
| 1313 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1314 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2); |
| 1315 |
break; |
| 1316 |
case rnemdPy : |
| 1317 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1318 |
+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2); |
| 1319 |
break; |
| 1320 |
case rnemdPz : |
| 1321 |
diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2) |
| 1322 |
+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2); |
| 1323 |
default : |
| 1324 |
break; |
| 1325 |
} |
| 1326 |
if (diff < smallestDiff) { |
| 1327 |
smallestDiff = diff; |
| 1328 |
bestPair = *rpi; |
| 1329 |
} |
| 1330 |
} |
| 1331 |
#ifdef IS_MPI |
| 1332 |
if (worldRank == 0) { |
| 1333 |
#endif |
| 1334 |
// sprintf(painCave.errMsg, |
| 1335 |
// "RNEMD: roots r1= %lf\tr2 = %lf\n", |
| 1336 |
// bestPair.first, bestPair.second); |
| 1337 |
// painCave.isFatal = 0; |
| 1338 |
// painCave.severity = OPENMD_INFO; |
| 1339 |
// simError(); |
| 1340 |
#ifdef IS_MPI |
| 1341 |
} |
| 1342 |
#endif |
| 1343 |
|
| 1344 |
switch(rnemdFluxType_) { |
| 1345 |
case rnemdKE : |
| 1346 |
x = bestPair.first; |
| 1347 |
y = bestPair.first; |
| 1348 |
z = bestPair.second; |
| 1349 |
break; |
| 1350 |
case rnemdPx : |
| 1351 |
x = c; |
| 1352 |
y = bestPair.first; |
| 1353 |
z = bestPair.second; |
| 1354 |
break; |
| 1355 |
case rnemdPy : |
| 1356 |
x = bestPair.first; |
| 1357 |
y = c; |
| 1358 |
z = bestPair.second; |
| 1359 |
break; |
| 1360 |
case rnemdPz : |
| 1361 |
x = bestPair.first; |
| 1362 |
y = bestPair.second; |
| 1363 |
z = c; |
| 1364 |
break; |
| 1365 |
default : |
| 1366 |
break; |
| 1367 |
} |
| 1368 |
vector<StuntDouble*>::iterator sdi; |
| 1369 |
Vector3d vel; |
| 1370 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1371 |
vel = (*sdi)->getVel(); |
| 1372 |
vel.x() *= x; |
| 1373 |
vel.y() *= y; |
| 1374 |
vel.z() *= z; |
| 1375 |
(*sdi)->setVel(vel); |
| 1376 |
} |
| 1377 |
//convert to hotBin coefficient |
| 1378 |
x = 1.0 + px * (1.0 - x); |
| 1379 |
y = 1.0 + py * (1.0 - y); |
| 1380 |
z = 1.0 + pz * (1.0 - z); |
| 1381 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1382 |
vel = (*sdi)->getVel(); |
| 1383 |
vel.x() *= x; |
| 1384 |
vel.y() *= y; |
| 1385 |
vel.z() *= z; |
| 1386 |
(*sdi)->setVel(vel); |
| 1387 |
} |
| 1388 |
successfulScale = true; |
| 1389 |
switch(rnemdFluxType_) { |
| 1390 |
case rnemdKE : |
| 1391 |
kineticExchange_ += kineticTarget_; |
| 1392 |
break; |
| 1393 |
case rnemdPx : |
| 1394 |
case rnemdPy : |
| 1395 |
case rnemdPz : |
| 1396 |
momentumExchange_ += momentumTarget_; |
| 1397 |
break; |
| 1398 |
default : |
| 1399 |
break; |
| 1400 |
} |
| 1401 |
} |
| 1402 |
} |
| 1403 |
if (successfulScale != true) { |
| 1404 |
sprintf(painCave.errMsg, |
| 1405 |
"RNEMD::doNIVS exchange NOT performed - roots that solve\n" |
| 1406 |
"\tthe constraint equations may not exist or there may be\n" |
| 1407 |
"\tno selected objects in one or both slabs.\n"); |
| 1408 |
painCave.isFatal = 0; |
| 1409 |
painCave.severity = OPENMD_INFO; |
| 1410 |
simError(); |
| 1411 |
failTrialCount_++; |
| 1412 |
} |
| 1413 |
} |
| 1414 |
|
| 1415 |
void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) { |
| 1416 |
if (!doRNEMD_) return; |
| 1417 |
int selei; |
| 1418 |
int selej; |
| 1419 |
|
| 1420 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1421 |
RealType time = currentSnap_->getTime(); |
| 1422 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1423 |
|
| 1424 |
StuntDouble* sd; |
| 1425 |
|
| 1426 |
vector<StuntDouble*> hotBin, coldBin; |
| 1427 |
|
| 1428 |
Vector3d Ph(V3Zero); |
| 1429 |
Vector3d Lh(V3Zero); |
| 1430 |
RealType Mh = 0.0; |
| 1431 |
Mat3x3d Ih(0.0); |
| 1432 |
RealType Kh = 0.0; |
| 1433 |
Vector3d Pc(V3Zero); |
| 1434 |
Vector3d Lc(V3Zero); |
| 1435 |
RealType Mc = 0.0; |
| 1436 |
Mat3x3d Ic(0.0); |
| 1437 |
RealType Kc = 0.0; |
| 1438 |
|
| 1439 |
for (sd = smanA.beginSelected(selei); sd != NULL; |
| 1440 |
sd = smanA.nextSelected(selei)) { |
| 1441 |
|
| 1442 |
Vector3d pos = sd->getPos(); |
| 1443 |
|
| 1444 |
// wrap the stuntdouble's position back into the box: |
| 1445 |
|
| 1446 |
if (usePeriodicBoundaryConditions_) |
| 1447 |
currentSnap_->wrapVector(pos); |
| 1448 |
|
| 1449 |
RealType mass = sd->getMass(); |
| 1450 |
Vector3d vel = sd->getVel(); |
| 1451 |
Vector3d rPos = sd->getPos() - coordinateOrigin_; |
| 1452 |
RealType r2; |
| 1453 |
|
| 1454 |
hotBin.push_back(sd); |
| 1455 |
Ph += mass * vel; |
| 1456 |
Mh += mass; |
| 1457 |
Kh += mass * vel.lengthSquare(); |
| 1458 |
Lh += mass * cross(rPos, vel); |
| 1459 |
Ih -= outProduct(rPos, rPos) * mass; |
| 1460 |
r2 = rPos.lengthSquare(); |
| 1461 |
Ih(0, 0) += mass * r2; |
| 1462 |
Ih(1, 1) += mass * r2; |
| 1463 |
Ih(2, 2) += mass * r2; |
| 1464 |
|
| 1465 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 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 |
Kh += angMom[j] * angMom[j] / I(j, j) + |
| 1474 |
angMom[k] * angMom[k] / I(k, k); |
| 1475 |
} else { |
| 1476 |
Kh += angMom[0] * angMom[0] / I(0, 0) + |
| 1477 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1478 |
angMom[2] * angMom[2] / I(2, 2); |
| 1479 |
} |
| 1480 |
} |
| 1481 |
} |
| 1482 |
} |
| 1483 |
for (sd = smanB.beginSelected(selej); sd != NULL; |
| 1484 |
sd = smanB.nextSelected(selej)) { |
| 1485 |
|
| 1486 |
Vector3d pos = sd->getPos(); |
| 1487 |
|
| 1488 |
// wrap the stuntdouble's position back into the box: |
| 1489 |
|
| 1490 |
if (usePeriodicBoundaryConditions_) |
| 1491 |
currentSnap_->wrapVector(pos); |
| 1492 |
|
| 1493 |
RealType mass = sd->getMass(); |
| 1494 |
Vector3d vel = sd->getVel(); |
| 1495 |
Vector3d rPos = sd->getPos() - coordinateOrigin_; |
| 1496 |
RealType r2; |
| 1497 |
|
| 1498 |
coldBin.push_back(sd); |
| 1499 |
Pc += mass * vel; |
| 1500 |
Mc += mass; |
| 1501 |
Kc += mass * vel.lengthSquare(); |
| 1502 |
Lc += mass * cross(rPos, vel); |
| 1503 |
Ic -= outProduct(rPos, rPos) * mass; |
| 1504 |
r2 = rPos.lengthSquare(); |
| 1505 |
Ic(0, 0) += mass * r2; |
| 1506 |
Ic(1, 1) += mass * r2; |
| 1507 |
Ic(2, 2) += mass * r2; |
| 1508 |
|
| 1509 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1510 |
if (sd->isDirectional()) { |
| 1511 |
Vector3d angMom = sd->getJ(); |
| 1512 |
Mat3x3d I = sd->getI(); |
| 1513 |
if (sd->isLinear()) { |
| 1514 |
int i = sd->linearAxis(); |
| 1515 |
int j = (i + 1) % 3; |
| 1516 |
int k = (i + 2) % 3; |
| 1517 |
Kc += angMom[j] * angMom[j] / I(j, j) + |
| 1518 |
angMom[k] * angMom[k] / I(k, k); |
| 1519 |
} else { |
| 1520 |
Kc += angMom[0] * angMom[0] / I(0, 0) + |
| 1521 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1522 |
angMom[2] * angMom[2] / I(2, 2); |
| 1523 |
} |
| 1524 |
} |
| 1525 |
} |
| 1526 |
} |
| 1527 |
|
| 1528 |
Kh *= 0.5; |
| 1529 |
Kc *= 0.5; |
| 1530 |
|
| 1531 |
#ifdef IS_MPI |
| 1532 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1533 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1534 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1535 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM); |
| 1536 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM); |
| 1537 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM); |
| 1538 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM); |
| 1539 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM); |
| 1540 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9, |
| 1541 |
MPI::REALTYPE, MPI::SUM); |
| 1542 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9, |
| 1543 |
MPI::REALTYPE, MPI::SUM); |
| 1544 |
#endif |
| 1545 |
|
| 1546 |
bool successfulExchange = false; |
| 1547 |
if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty |
| 1548 |
Vector3d vc = Pc / Mc; |
| 1549 |
Vector3d ac = -momentumTarget_ / Mc + vc; |
| 1550 |
Vector3d acrec = -momentumTarget_ / Mc; |
| 1551 |
|
| 1552 |
// We now need the inverse of the inertia tensor to calculate the |
| 1553 |
// angular velocity of the cold slab; |
| 1554 |
Mat3x3d Ici = Ic.inverse(); |
| 1555 |
Vector3d omegac = Ici * Lc; |
| 1556 |
Vector3d bc = -(Ici * angularMomentumTarget_) + omegac; |
| 1557 |
Vector3d bcrec = bc - omegac; |
| 1558 |
|
| 1559 |
RealType cNumerator = Kc - kineticTarget_ |
| 1560 |
- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc)); |
| 1561 |
if (cNumerator > 0.0) { |
| 1562 |
|
| 1563 |
RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare() |
| 1564 |
- 0.5*(dot(omegac, Ic * omegac)); |
| 1565 |
|
| 1566 |
if (cDenominator > 0.0) { |
| 1567 |
RealType c = sqrt(cNumerator / cDenominator); |
| 1568 |
if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients |
| 1569 |
|
| 1570 |
Vector3d vh = Ph / Mh; |
| 1571 |
Vector3d ah = momentumTarget_ / Mh + vh; |
| 1572 |
Vector3d ahrec = momentumTarget_ / Mh; |
| 1573 |
|
| 1574 |
// We now need the inverse of the inertia tensor to |
| 1575 |
// calculate the angular velocity of the hot slab; |
| 1576 |
Mat3x3d Ihi = Ih.inverse(); |
| 1577 |
Vector3d omegah = Ihi * Lh; |
| 1578 |
Vector3d bh = (Ihi * angularMomentumTarget_) + omegah; |
| 1579 |
Vector3d bhrec = bh - omegah; |
| 1580 |
|
| 1581 |
RealType hNumerator = Kh + kineticTarget_ |
| 1582 |
- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));; |
| 1583 |
if (hNumerator > 0.0) { |
| 1584 |
|
| 1585 |
RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare() |
| 1586 |
- 0.5*(dot(omegah, Ih * omegah)); |
| 1587 |
|
| 1588 |
if (hDenominator > 0.0) { |
| 1589 |
RealType h = sqrt(hNumerator / hDenominator); |
| 1590 |
if ((h > 0.9) && (h < 1.1)) { |
| 1591 |
|
| 1592 |
vector<StuntDouble*>::iterator sdi; |
| 1593 |
Vector3d vel; |
| 1594 |
Vector3d rPos; |
| 1595 |
|
| 1596 |
for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) { |
| 1597 |
//vel = (*sdi)->getVel(); |
| 1598 |
rPos = (*sdi)->getPos() - coordinateOrigin_; |
| 1599 |
vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c |
| 1600 |
+ ac + cross(bc, rPos); |
| 1601 |
(*sdi)->setVel(vel); |
| 1602 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1603 |
if ((*sdi)->isDirectional()) { |
| 1604 |
Vector3d angMom = (*sdi)->getJ() * c; |
| 1605 |
(*sdi)->setJ(angMom); |
| 1606 |
} |
| 1607 |
} |
| 1608 |
} |
| 1609 |
for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) { |
| 1610 |
//vel = (*sdi)->getVel(); |
| 1611 |
rPos = (*sdi)->getPos() - coordinateOrigin_; |
| 1612 |
vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h |
| 1613 |
+ ah + cross(bh, rPos); |
| 1614 |
(*sdi)->setVel(vel); |
| 1615 |
if (rnemdFluxType_ == rnemdFullKE) { |
| 1616 |
if ((*sdi)->isDirectional()) { |
| 1617 |
Vector3d angMom = (*sdi)->getJ() * h; |
| 1618 |
(*sdi)->setJ(angMom); |
| 1619 |
} |
| 1620 |
} |
| 1621 |
} |
| 1622 |
successfulExchange = true; |
| 1623 |
kineticExchange_ += kineticTarget_; |
| 1624 |
momentumExchange_ += momentumTarget_; |
| 1625 |
angularMomentumExchange_ += angularMomentumTarget_; |
| 1626 |
} |
| 1627 |
} |
| 1628 |
} |
| 1629 |
} |
| 1630 |
} |
| 1631 |
} |
| 1632 |
} |
| 1633 |
if (successfulExchange != true) { |
| 1634 |
sprintf(painCave.errMsg, |
| 1635 |
"RNEMD::doVSS exchange NOT performed - roots that solve\n" |
| 1636 |
"\tthe constraint equations may not exist or there may be\n" |
| 1637 |
"\tno selected objects in one or both slabs.\n"); |
| 1638 |
painCave.isFatal = 0; |
| 1639 |
painCave.severity = OPENMD_INFO; |
| 1640 |
simError(); |
| 1641 |
failTrialCount_++; |
| 1642 |
} |
| 1643 |
} |
| 1644 |
|
| 1645 |
RealType RNEMD::getDividingArea() { |
| 1646 |
|
| 1647 |
if (hasDividingArea_) return dividingArea_; |
| 1648 |
|
| 1649 |
RealType areaA, areaB; |
| 1650 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1651 |
|
| 1652 |
if (hasSelectionA_) { |
| 1653 |
int isd; |
| 1654 |
StuntDouble* sd; |
| 1655 |
vector<StuntDouble*> aSites; |
| 1656 |
ConvexHull* surfaceMeshA = new ConvexHull(); |
| 1657 |
seleManA_.setSelectionSet(evaluatorA_.evaluate()); |
| 1658 |
for (sd = seleManA_.beginSelected(isd); sd != NULL; |
| 1659 |
sd = seleManA_.nextSelected(isd)) { |
| 1660 |
aSites.push_back(sd); |
| 1661 |
} |
| 1662 |
surfaceMeshA->computeHull(aSites); |
| 1663 |
areaA = surfaceMeshA->getArea(); |
| 1664 |
} else { |
| 1665 |
if (usePeriodicBoundaryConditions_) { |
| 1666 |
// in periodic boundaries, the surface area is twice the x-y |
| 1667 |
// area of the current box: |
| 1668 |
areaA = 2.0 * snap->getXYarea(); |
| 1669 |
} else { |
| 1670 |
// in non-periodic simulations, without explicitly setting |
| 1671 |
// selections, the sphere radius sets the surface area of the |
| 1672 |
// dividing surface: |
| 1673 |
areaA = 4.0 * M_PI * pow(sphereARadius_, 2); |
| 1674 |
} |
| 1675 |
} |
| 1676 |
|
| 1677 |
if (hasSelectionB_) { |
| 1678 |
int isd; |
| 1679 |
StuntDouble* sd; |
| 1680 |
vector<StuntDouble*> bSites; |
| 1681 |
ConvexHull* surfaceMeshB = new ConvexHull(); |
| 1682 |
seleManB_.setSelectionSet(evaluatorB_.evaluate()); |
| 1683 |
for (sd = seleManB_.beginSelected(isd); sd != NULL; |
| 1684 |
sd = seleManB_.nextSelected(isd)) { |
| 1685 |
bSites.push_back(sd); |
| 1686 |
} |
| 1687 |
surfaceMeshB->computeHull(bSites); |
| 1688 |
areaB = surfaceMeshB->getArea(); |
| 1689 |
} else { |
| 1690 |
if (usePeriodicBoundaryConditions_) { |
| 1691 |
// in periodic boundaries, the surface area is twice the x-y |
| 1692 |
// area of the current box: |
| 1693 |
areaB = 2.0 * snap->getXYarea(); |
| 1694 |
} else { |
| 1695 |
// in non-periodic simulations, without explicitly setting |
| 1696 |
// selections, but if a sphereBradius has been set, just use that: |
| 1697 |
areaB = 4.0 * M_PI * pow(sphereBRadius_, 2); |
| 1698 |
} |
| 1699 |
} |
| 1700 |
|
| 1701 |
dividingArea_ = min(areaA, areaB); |
| 1702 |
hasDividingArea_ = true; |
| 1703 |
return dividingArea_; |
| 1704 |
} |
| 1705 |
|
| 1706 |
void RNEMD::doRNEMD() { |
| 1707 |
if (!doRNEMD_) return; |
| 1708 |
trialCount_++; |
| 1709 |
|
| 1710 |
// object evaluator: |
| 1711 |
evaluator_.loadScriptString(rnemdObjectSelection_); |
| 1712 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 1713 |
|
| 1714 |
evaluatorA_.loadScriptString(selectionA_); |
| 1715 |
evaluatorB_.loadScriptString(selectionB_); |
| 1716 |
|
| 1717 |
seleManA_.setSelectionSet(evaluatorA_.evaluate()); |
| 1718 |
seleManB_.setSelectionSet(evaluatorB_.evaluate()); |
| 1719 |
|
| 1720 |
commonA_ = seleManA_ & seleMan_; |
| 1721 |
commonB_ = seleManB_ & seleMan_; |
| 1722 |
|
| 1723 |
// Target exchange quantities (in each exchange) = dividingArea * dt * flux |
| 1724 |
// dt = exchange time interval |
| 1725 |
// flux = target flux |
| 1726 |
// dividingArea = smallest dividing surface between the two regions |
| 1727 |
|
| 1728 |
hasDividingArea_ = false; |
| 1729 |
RealType area = getDividingArea(); |
| 1730 |
|
| 1731 |
kineticTarget_ = kineticFlux_ * exchangeTime_ * area; |
| 1732 |
momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area; |
| 1733 |
angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area; |
| 1734 |
|
| 1735 |
switch(rnemdMethod_) { |
| 1736 |
case rnemdSwap: |
| 1737 |
doSwap(commonA_, commonB_); |
| 1738 |
break; |
| 1739 |
case rnemdNIVS: |
| 1740 |
doNIVS(commonA_, commonB_); |
| 1741 |
break; |
| 1742 |
case rnemdVSS: |
| 1743 |
doVSS(commonA_, commonB_); |
| 1744 |
break; |
| 1745 |
case rnemdUnkownMethod: |
| 1746 |
default : |
| 1747 |
break; |
| 1748 |
} |
| 1749 |
} |
| 1750 |
|
| 1751 |
void RNEMD::collectData() { |
| 1752 |
if (!doRNEMD_) return; |
| 1753 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1754 |
|
| 1755 |
// collectData can be called more frequently than the doRNEMD, so use the |
| 1756 |
// computed area from the last exchange time: |
| 1757 |
|
| 1758 |
areaAccumulator_->add(getDividingArea()); |
| 1759 |
Mat3x3d hmat = currentSnap_->getHmat(); |
| 1760 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 1761 |
|
| 1762 |
int selei(0); |
| 1763 |
StuntDouble* sd; |
| 1764 |
int binNo; |
| 1765 |
|
| 1766 |
vector<RealType> binMass(nBins_, 0.0); |
| 1767 |
vector<RealType> binPx(nBins_, 0.0); |
| 1768 |
vector<RealType> binPy(nBins_, 0.0); |
| 1769 |
vector<RealType> binPz(nBins_, 0.0); |
| 1770 |
vector<RealType> binOmegax(nBins_, 0.0); |
| 1771 |
vector<RealType> binOmegay(nBins_, 0.0); |
| 1772 |
vector<RealType> binOmegaz(nBins_, 0.0); |
| 1773 |
vector<RealType> binKE(nBins_, 0.0); |
| 1774 |
vector<int> binDOF(nBins_, 0); |
| 1775 |
vector<int> binCount(nBins_, 0); |
| 1776 |
|
| 1777 |
// alternative approach, track all molecules instead of only those |
| 1778 |
// selected for scaling/swapping: |
| 1779 |
/* |
| 1780 |
SimInfo::MoleculeIterator miter; |
| 1781 |
vector<StuntDouble*>::iterator iiter; |
| 1782 |
Molecule* mol; |
| 1783 |
StuntDouble* sd; |
| 1784 |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 1785 |
mol = info_->nextMolecule(miter)) |
| 1786 |
sd is essentially sd |
| 1787 |
for (sd = mol->beginIntegrableObject(iiter); |
| 1788 |
sd != NULL; |
| 1789 |
sd = mol->nextIntegrableObject(iiter)) |
| 1790 |
*/ |
| 1791 |
|
| 1792 |
for (sd = seleMan_.beginSelected(selei); sd != NULL; |
| 1793 |
sd = seleMan_.nextSelected(selei)) { |
| 1794 |
|
| 1795 |
Vector3d pos = sd->getPos(); |
| 1796 |
|
| 1797 |
// wrap the stuntdouble's position back into the box: |
| 1798 |
|
| 1799 |
if (usePeriodicBoundaryConditions_) { |
| 1800 |
currentSnap_->wrapVector(pos); |
| 1801 |
// which bin is this stuntdouble in? |
| 1802 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 1803 |
// Shift molecules by half a box to have bins start at 0 |
| 1804 |
// The modulo operator is used to wrap the case when we are |
| 1805 |
// beyond the end of the bins back to the beginning. |
| 1806 |
binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_; |
| 1807 |
} else { |
| 1808 |
Vector3d rPos = pos - coordinateOrigin_; |
| 1809 |
binNo = int(rPos.length() / binWidth_); |
| 1810 |
} |
| 1811 |
|
| 1812 |
RealType mass = sd->getMass(); |
| 1813 |
Vector3d vel = sd->getVel(); |
| 1814 |
Vector3d rPos = sd->getPos() - coordinateOrigin_; |
| 1815 |
Vector3d aVel = cross(rPos, vel); |
| 1816 |
|
| 1817 |
if (binNo < nBins_) { |
| 1818 |
binCount[binNo]++; |
| 1819 |
binMass[binNo] += mass; |
| 1820 |
binPx[binNo] += mass*vel.x(); |
| 1821 |
binPy[binNo] += mass*vel.y(); |
| 1822 |
binPz[binNo] += mass*vel.z(); |
| 1823 |
binOmegax[binNo] += aVel.x(); |
| 1824 |
binOmegay[binNo] += aVel.y(); |
| 1825 |
binOmegaz[binNo] += aVel.z(); |
| 1826 |
binKE[binNo] += 0.5 * (mass * vel.lengthSquare()); |
| 1827 |
binDOF[binNo] += 3; |
| 1828 |
|
| 1829 |
if (sd->isDirectional()) { |
| 1830 |
Vector3d angMom = sd->getJ(); |
| 1831 |
Mat3x3d I = sd->getI(); |
| 1832 |
if (sd->isLinear()) { |
| 1833 |
int i = sd->linearAxis(); |
| 1834 |
int j = (i + 1) % 3; |
| 1835 |
int k = (i + 2) % 3; |
| 1836 |
binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) + |
| 1837 |
angMom[k] * angMom[k] / I(k, k)); |
| 1838 |
binDOF[binNo] += 2; |
| 1839 |
} else { |
| 1840 |
binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) + |
| 1841 |
angMom[1] * angMom[1] / I(1, 1) + |
| 1842 |
angMom[2] * angMom[2] / I(2, 2)); |
| 1843 |
binDOF[binNo] += 3; |
| 1844 |
} |
| 1845 |
} |
| 1846 |
} |
| 1847 |
} |
| 1848 |
|
| 1849 |
#ifdef IS_MPI |
| 1850 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0], |
| 1851 |
nBins_, MPI::INT, MPI::SUM); |
| 1852 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0], |
| 1853 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1854 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0], |
| 1855 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1856 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0], |
| 1857 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1858 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0], |
| 1859 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1860 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0], |
| 1861 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1862 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0], |
| 1863 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1864 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0], |
| 1865 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1866 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0], |
| 1867 |
nBins_, MPI::REALTYPE, MPI::SUM); |
| 1868 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0], |
| 1869 |
nBins_, MPI::INT, MPI::SUM); |
| 1870 |
#endif |
| 1871 |
|
| 1872 |
Vector3d vel; |
| 1873 |
Vector3d aVel; |
| 1874 |
RealType den; |
| 1875 |
RealType temp; |
| 1876 |
RealType z; |
| 1877 |
RealType r; |
| 1878 |
for (int i = 0; i < nBins_; i++) { |
| 1879 |
if (usePeriodicBoundaryConditions_) { |
| 1880 |
z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2); |
| 1881 |
den = binMass[i] * nBins_ * PhysicalConstants::densityConvert |
| 1882 |
/ currentSnap_->getVolume() ; |
| 1883 |
} else { |
| 1884 |
r = (((RealType)i + 0.5) * binWidth_); |
| 1885 |
RealType rinner = (RealType)i * binWidth_; |
| 1886 |
RealType router = (RealType)(i+1) * binWidth_; |
| 1887 |
den = binMass[i] * 3.0 * PhysicalConstants::densityConvert |
| 1888 |
/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3))); |
| 1889 |
} |
| 1890 |
vel.x() = binPx[i] / binMass[i]; |
| 1891 |
vel.y() = binPy[i] / binMass[i]; |
| 1892 |
vel.z() = binPz[i] / binMass[i]; |
| 1893 |
aVel.x() = binOmegax[i]; |
| 1894 |
aVel.y() = binOmegay[i]; |
| 1895 |
aVel.z() = binOmegaz[i]; |
| 1896 |
|
| 1897 |
if (binCount[i] > 0) { |
| 1898 |
// only add values if there are things to add |
| 1899 |
temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb * |
| 1900 |
PhysicalConstants::energyConvert); |
| 1901 |
|
| 1902 |
for (unsigned int j = 0; j < outputMask_.size(); ++j) { |
| 1903 |
if(outputMask_[j]) { |
| 1904 |
switch(j) { |
| 1905 |
case Z: |
| 1906 |
dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z); |
| 1907 |
break; |
| 1908 |
case R: |
| 1909 |
dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r); |
| 1910 |
break; |
| 1911 |
case TEMPERATURE: |
| 1912 |
dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp); |
| 1913 |
break; |
| 1914 |
case VELOCITY: |
| 1915 |
dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel); |
| 1916 |
break; |
| 1917 |
case ANGULARVELOCITY: |
| 1918 |
dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel); |
| 1919 |
break; |
| 1920 |
case DENSITY: |
| 1921 |
dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den); |
| 1922 |
break; |
| 1923 |
} |
| 1924 |
} |
| 1925 |
} |
| 1926 |
} |
| 1927 |
} |
| 1928 |
} |
| 1929 |
|
| 1930 |
void RNEMD::getStarted() { |
| 1931 |
if (!doRNEMD_) return; |
| 1932 |
hasDividingArea_ = false; |
| 1933 |
collectData(); |
| 1934 |
writeOutputFile(); |
| 1935 |
} |
| 1936 |
|
| 1937 |
void RNEMD::parseOutputFileFormat(const std::string& format) { |
| 1938 |
if (!doRNEMD_) return; |
| 1939 |
StringTokenizer tokenizer(format, " ,;|\t\n\r"); |
| 1940 |
|
| 1941 |
while(tokenizer.hasMoreTokens()) { |
| 1942 |
std::string token(tokenizer.nextToken()); |
| 1943 |
toUpper(token); |
| 1944 |
OutputMapType::iterator i = outputMap_.find(token); |
| 1945 |
if (i != outputMap_.end()) { |
| 1946 |
outputMask_.set(i->second); |
| 1947 |
} else { |
| 1948 |
sprintf( painCave.errMsg, |
| 1949 |
"RNEMD::parseOutputFileFormat: %s is not a recognized\n" |
| 1950 |
"\toutputFileFormat keyword.\n", token.c_str() ); |
| 1951 |
painCave.isFatal = 0; |
| 1952 |
painCave.severity = OPENMD_ERROR; |
| 1953 |
simError(); |
| 1954 |
} |
| 1955 |
} |
| 1956 |
} |
| 1957 |
|
| 1958 |
void RNEMD::writeOutputFile() { |
| 1959 |
if (!doRNEMD_) return; |
| 1960 |
|
| 1961 |
#ifdef IS_MPI |
| 1962 |
// If we're the root node, should we print out the results |
| 1963 |
int worldRank = MPI::COMM_WORLD.Get_rank(); |
| 1964 |
if (worldRank == 0) { |
| 1965 |
#endif |
| 1966 |
rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc ); |
| 1967 |
|
| 1968 |
if( !rnemdFile_ ){ |
| 1969 |
sprintf( painCave.errMsg, |
| 1970 |
"Could not open \"%s\" for RNEMD output.\n", |
| 1971 |
rnemdFileName_.c_str()); |
| 1972 |
painCave.isFatal = 1; |
| 1973 |
simError(); |
| 1974 |
} |
| 1975 |
|
| 1976 |
Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1977 |
|
| 1978 |
RealType time = currentSnap_->getTime(); |
| 1979 |
RealType avgArea; |
| 1980 |
areaAccumulator_->getAverage(avgArea); |
| 1981 |
RealType Jz = kineticExchange_ / (time * avgArea) |
| 1982 |
/ PhysicalConstants::energyConvert; |
| 1983 |
Vector3d JzP = momentumExchange_ / (time * avgArea); |
| 1984 |
Vector3d JzL = angularMomentumExchange_ / (time * avgArea); |
| 1985 |
|
| 1986 |
rnemdFile_ << "#######################################################\n"; |
| 1987 |
rnemdFile_ << "# RNEMD {\n"; |
| 1988 |
|
| 1989 |
map<string, RNEMDMethod>::iterator mi; |
| 1990 |
for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) { |
| 1991 |
if ( (*mi).second == rnemdMethod_) |
| 1992 |
rnemdFile_ << "# exchangeMethod = \"" << (*mi).first << "\";\n"; |
| 1993 |
} |
| 1994 |
map<string, RNEMDFluxType>::iterator fi; |
| 1995 |
for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) { |
| 1996 |
if ( (*fi).second == rnemdFluxType_) |
| 1997 |
rnemdFile_ << "# fluxType = \"" << (*fi).first << "\";\n"; |
| 1998 |
} |
| 1999 |
|
| 2000 |
rnemdFile_ << "# exchangeTime = " << exchangeTime_ << ";\n"; |
| 2001 |
|
| 2002 |
rnemdFile_ << "# objectSelection = \"" |
| 2003 |
<< rnemdObjectSelection_ << "\";\n"; |
| 2004 |
rnemdFile_ << "# selectionA = \"" << selectionA_ << "\";\n"; |
| 2005 |
rnemdFile_ << "# selectionB = \"" << selectionB_ << "\";\n"; |
| 2006 |
rnemdFile_ << "# }\n"; |
| 2007 |
rnemdFile_ << "#######################################################\n"; |
| 2008 |
rnemdFile_ << "# RNEMD report:\n"; |
| 2009 |
rnemdFile_ << "# running time = " << time << " fs\n"; |
| 2010 |
rnemdFile_ << "# Target flux:\n"; |
| 2011 |
rnemdFile_ << "# kinetic = " |
| 2012 |
<< kineticFlux_ / PhysicalConstants::energyConvert |
| 2013 |
<< " (kcal/mol/A^2/fs)\n"; |
| 2014 |
rnemdFile_ << "# momentum = " << momentumFluxVector_ |
| 2015 |
<< " (amu/A/fs^2)\n"; |
| 2016 |
rnemdFile_ << "# angular momentum = " << angularMomentumFluxVector_ |
| 2017 |
<< " (amu/A^2/fs^2)\n"; |
| 2018 |
rnemdFile_ << "# Target one-time exchanges:\n"; |
| 2019 |
rnemdFile_ << "# kinetic = " |
| 2020 |
<< kineticTarget_ / PhysicalConstants::energyConvert |
| 2021 |
<< " (kcal/mol)\n"; |
| 2022 |
rnemdFile_ << "# momentum = " << momentumTarget_ |
| 2023 |
<< " (amu*A/fs)\n"; |
| 2024 |
rnemdFile_ << "# angular momentum = " << angularMomentumTarget_ |
| 2025 |
<< " (amu*A^2/fs)\n"; |
| 2026 |
rnemdFile_ << "# Actual exchange totals:\n"; |
| 2027 |
rnemdFile_ << "# kinetic = " |
| 2028 |
<< kineticExchange_ / PhysicalConstants::energyConvert |
| 2029 |
<< " (kcal/mol)\n"; |
| 2030 |
rnemdFile_ << "# momentum = " << momentumExchange_ |
| 2031 |
<< " (amu*A/fs)\n"; |
| 2032 |
rnemdFile_ << "# angular momentum = " << angularMomentumExchange_ |
| 2033 |
<< " (amu*A^2/fs)\n"; |
| 2034 |
rnemdFile_ << "# Actual flux:\n"; |
| 2035 |
rnemdFile_ << "# kinetic = " << Jz |
| 2036 |
<< " (kcal/mol/A^2/fs)\n"; |
| 2037 |
rnemdFile_ << "# momentum = " << JzP |
| 2038 |
<< " (amu/A/fs^2)\n"; |
| 2039 |
rnemdFile_ << "# angular momentum = " << JzL |
| 2040 |
<< " (amu/A^2/fs^2)\n"; |
| 2041 |
rnemdFile_ << "# Exchange statistics:\n"; |
| 2042 |
rnemdFile_ << "# attempted = " << trialCount_ << "\n"; |
| 2043 |
rnemdFile_ << "# failed = " << failTrialCount_ << "\n"; |
| 2044 |
if (rnemdMethod_ == rnemdNIVS) { |
| 2045 |
rnemdFile_ << "# NIVS root-check errors = " |
| 2046 |
<< failRootCount_ << "\n"; |
| 2047 |
} |
| 2048 |
rnemdFile_ << "#######################################################\n"; |
| 2049 |
|
| 2050 |
|
| 2051 |
|
| 2052 |
//write title |
| 2053 |
rnemdFile_ << "#"; |
| 2054 |
for (unsigned int i = 0; i < outputMask_.size(); ++i) { |
| 2055 |
if (outputMask_[i]) { |
| 2056 |
rnemdFile_ << "\t" << data_[i].title << |
| 2057 |
"(" << data_[i].units << ")"; |
| 2058 |
// add some extra tabs for column alignment |
| 2059 |
if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t"; |
| 2060 |
} |
| 2061 |
} |
| 2062 |
rnemdFile_ << std::endl; |
| 2063 |
|
| 2064 |
rnemdFile_.precision(8); |
| 2065 |
|
| 2066 |
for (int j = 0; j < nBins_; j++) { |
| 2067 |
|
| 2068 |
for (unsigned int i = 0; i < outputMask_.size(); ++i) { |
| 2069 |
if (outputMask_[i]) { |
| 2070 |
if (data_[i].dataType == "RealType") |
| 2071 |
writeReal(i,j); |
| 2072 |
else if (data_[i].dataType == "Vector3d") |
| 2073 |
writeVector(i,j); |
| 2074 |
else { |
| 2075 |
sprintf( painCave.errMsg, |
| 2076 |
"RNEMD found an unknown data type for: %s ", |
| 2077 |
data_[i].title.c_str()); |
| 2078 |
painCave.isFatal = 1; |
| 2079 |
simError(); |
| 2080 |
} |
| 2081 |
} |
| 2082 |
} |
| 2083 |
rnemdFile_ << std::endl; |
| 2084 |
|
| 2085 |
} |
| 2086 |
|
| 2087 |
rnemdFile_ << "#######################################################\n"; |
| 2088 |
rnemdFile_ << "# Standard Deviations in those quantities follow:\n"; |
| 2089 |
rnemdFile_ << "#######################################################\n"; |
| 2090 |
|
| 2091 |
|
| 2092 |
for (int j = 0; j < nBins_; j++) { |
| 2093 |
rnemdFile_ << "#"; |
| 2094 |
for (unsigned int i = 0; i < outputMask_.size(); ++i) { |
| 2095 |
if (outputMask_[i]) { |
| 2096 |
if (data_[i].dataType == "RealType") |
| 2097 |
writeRealStdDev(i,j); |
| 2098 |
else if (data_[i].dataType == "Vector3d") |
| 2099 |
writeVectorStdDev(i,j); |
| 2100 |
else { |
| 2101 |
sprintf( painCave.errMsg, |
| 2102 |
"RNEMD found an unknown data type for: %s ", |
| 2103 |
data_[i].title.c_str()); |
| 2104 |
painCave.isFatal = 1; |
| 2105 |
simError(); |
| 2106 |
} |
| 2107 |
} |
| 2108 |
} |
| 2109 |
rnemdFile_ << std::endl; |
| 2110 |
|
| 2111 |
} |
| 2112 |
|
| 2113 |
rnemdFile_.flush(); |
| 2114 |
rnemdFile_.close(); |
| 2115 |
|
| 2116 |
#ifdef IS_MPI |
| 2117 |
} |
| 2118 |
#endif |
| 2119 |
|
| 2120 |
} |
| 2121 |
|
| 2122 |
void RNEMD::writeReal(int index, unsigned int bin) { |
| 2123 |
if (!doRNEMD_) return; |
| 2124 |
assert(index >=0 && index < ENDINDEX); |
| 2125 |
assert(int(bin) < nBins_); |
| 2126 |
RealType s; |
| 2127 |
int count; |
| 2128 |
|
| 2129 |
count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count(); |
| 2130 |
if (count == 0) return; |
| 2131 |
|
| 2132 |
dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s); |
| 2133 |
|
| 2134 |
if (! isinf(s) && ! isnan(s)) { |
| 2135 |
rnemdFile_ << "\t" << s; |
| 2136 |
} else{ |
| 2137 |
sprintf( painCave.errMsg, |
| 2138 |
"RNEMD detected a numerical error writing: %s for bin %d", |
| 2139 |
data_[index].title.c_str(), bin); |
| 2140 |
painCave.isFatal = 1; |
| 2141 |
simError(); |
| 2142 |
} |
| 2143 |
} |
| 2144 |
|
| 2145 |
void RNEMD::writeVector(int index, unsigned int bin) { |
| 2146 |
if (!doRNEMD_) return; |
| 2147 |
assert(index >=0 && index < ENDINDEX); |
| 2148 |
assert(int(bin) < nBins_); |
| 2149 |
Vector3d s; |
| 2150 |
int count; |
| 2151 |
|
| 2152 |
count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count(); |
| 2153 |
if (count == 0) return; |
| 2154 |
|
| 2155 |
dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s); |
| 2156 |
if (isinf(s[0]) || isnan(s[0]) || |
| 2157 |
isinf(s[1]) || isnan(s[1]) || |
| 2158 |
isinf(s[2]) || isnan(s[2]) ) { |
| 2159 |
sprintf( painCave.errMsg, |
| 2160 |
"RNEMD detected a numerical error writing: %s for bin %d", |
| 2161 |
data_[index].title.c_str(), bin); |
| 2162 |
painCave.isFatal = 1; |
| 2163 |
simError(); |
| 2164 |
} else { |
| 2165 |
rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; |
| 2166 |
} |
| 2167 |
} |
| 2168 |
|
| 2169 |
void RNEMD::writeRealStdDev(int index, unsigned int bin) { |
| 2170 |
if (!doRNEMD_) return; |
| 2171 |
assert(index >=0 && index < ENDINDEX); |
| 2172 |
assert(int(bin) < nBins_); |
| 2173 |
RealType s; |
| 2174 |
int count; |
| 2175 |
|
| 2176 |
count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count(); |
| 2177 |
if (count == 0) return; |
| 2178 |
|
| 2179 |
dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s); |
| 2180 |
|
| 2181 |
if (! isinf(s) && ! isnan(s)) { |
| 2182 |
rnemdFile_ << "\t" << s; |
| 2183 |
} else{ |
| 2184 |
sprintf( painCave.errMsg, |
| 2185 |
"RNEMD detected a numerical error writing: %s std. dev. for bin %d", |
| 2186 |
data_[index].title.c_str(), bin); |
| 2187 |
painCave.isFatal = 1; |
| 2188 |
simError(); |
| 2189 |
} |
| 2190 |
} |
| 2191 |
|
| 2192 |
void RNEMD::writeVectorStdDev(int index, unsigned int bin) { |
| 2193 |
if (!doRNEMD_) return; |
| 2194 |
assert(index >=0 && index < ENDINDEX); |
| 2195 |
assert(int(bin) < nBins_); |
| 2196 |
Vector3d s; |
| 2197 |
int count; |
| 2198 |
|
| 2199 |
count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count(); |
| 2200 |
if (count == 0) return; |
| 2201 |
|
| 2202 |
dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s); |
| 2203 |
if (isinf(s[0]) || isnan(s[0]) || |
| 2204 |
isinf(s[1]) || isnan(s[1]) || |
| 2205 |
isinf(s[2]) || isnan(s[2]) ) { |
| 2206 |
sprintf( painCave.errMsg, |
| 2207 |
"RNEMD detected a numerical error writing: %s std. dev. for bin %d", |
| 2208 |
data_[index].title.c_str(), bin); |
| 2209 |
painCave.isFatal = 1; |
| 2210 |
simError(); |
| 2211 |
} else { |
| 2212 |
rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2]; |
| 2213 |
} |
| 2214 |
} |
| 2215 |
} |
| 2216 |
|
