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/* |
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* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |
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*/ |
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|
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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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#include <fstream> |
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#include <iostream> |
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#include <locale> |
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#include "utils/simError.h" |
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#include "utils/CaseConversion.hpp" |
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#include "brains/Register.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "constraints/ZconstraintForceManager.hpp" |
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#include "restraints/RestraintForceManager.hpp" |
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#include "integrators/IntegratorFactory.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "optimization/OptimizationFactory.hpp" |
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#include "optimization/Method.hpp" |
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#include "optimization/Constraint.hpp" |
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#include "optimization/Problem.hpp" |
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#include "optimization/PotentialEnergyObjectiveFunction.hpp" |
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#include "restraints/ThermoIntegrationForceManager.hpp" |
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|
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using namespace OpenMD; |
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using namespace QuantLib; |
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|
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int main(int argc,char* argv[]){ |
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|
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// first things first, all of the initializations |
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|
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#ifdef IS_MPI |
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MPI_Init( &argc, &argv ); // the MPI communicators |
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#endif |
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|
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initSimError(); // the error handler |
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//srand48( 1337 ); // the random number generator. |
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|
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std::string svnrev; |
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//convert a macro from compiler to a string in c++ |
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STR_DEFINE(svnrev, SVN_REV ); |
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|
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std::string revision; |
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|
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if (!svnrev.empty()) { |
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revision.assign(" Revision: " + svnrev); |
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} |
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|
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revision.resize(19,' '); |
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|
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
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std::cerr << |
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" +--------------------------------------------------------------------------+\n"<< |
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" | ____ __ ___ ____ |\n"<< |
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" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
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" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
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" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
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" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2012 by the |\n"<< |
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" | /_/ University of Notre Dame. |\n"<< |
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" | |\n"<< |
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" | version " << |
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OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << revision << |
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" http://www.openmd.net |\n"<< |
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" | |\n"<< |
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" | OpenMD is an OpenScience project. All source code is available for any |\n"<< |
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" | use whatsoever under a BSD-style license. |\n"<< |
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" | |\n"<< |
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" | Support OpenScience! If you use OpenMD or its source code in your |\n"<< |
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" | research, please cite the appropriate papers when you publish your work |\n"<< |
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" | Good starting points are: |\n"<< |
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" | |\n"<< |
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" | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n"<< |
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" | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n"<< |
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" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |\n"<< |
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" | [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |\n"<< |
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" | [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n"<< |
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" | [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |\n"<< |
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" +--------------------------------------------------------------------------+\n"<< |
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"\n"; |
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|
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if( argc < 2 ){ |
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strcpy( painCave.errMsg, "Error, a meta-data file is needed to run.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef IS_MPI |
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} |
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#endif |
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|
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strcpy( checkPointMsg, "Successful number of arguments" ); |
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errorCheckPoint(); |
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|
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//register forcefields, integrators and minimizers |
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registerAll(); |
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|
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//create simulation model |
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SimCreator creator; |
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SimInfo* info = creator.createSim(argv[1]); |
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|
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Globals* simParams = info->getSimParams(); |
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MinimizerParameters* miniPars = simParams->getMinimizerParameters(); |
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|
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if (miniPars->getUseMinimizer() && simParams->haveEnsemble()) { |
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sprintf(painCave.errMsg, "Ensemble keyword can not co-exist with useMinimizer = \"true\" in the minimizer block\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (miniPars->getUseMinimizer()) { |
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//create minimizer |
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OptimizationMethod* myMinimizer =OptimizationFactory::getInstance()->createOptimization(toUpperCopy(miniPars->getMethod()), info); |
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|
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if (myMinimizer == NULL) { |
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sprintf(painCave.errMsg, "Optimization Factory can not create %s OptimizationMethod\n", |
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miniPars->getMethod().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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ForceManager* fman = new ForceManager(info); |
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fman->initialize(); |
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|
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PotentialEnergyObjectiveFunction potObjf(info, fman); |
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DumpStatusFunction dsf(info); |
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DynamicVector<RealType> initCoords = potObjf.setInitialCoords(); |
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Problem problem(potObjf, *(new NoConstraint()), dsf, initCoords); |
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|
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|
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int maxIter = miniPars->getMaxIterations(); |
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int mssIter = miniPars->getMaxStationaryStateIterations(); |
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RealType rEps = miniPars->getRootEpsilon(); |
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RealType fEps = miniPars->getFunctionEpsilon(); |
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RealType gnEps = miniPars->getGradientNormEpsilon(); |
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|
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EndCriteria endCriteria(maxIter, mssIter, rEps, fEps, gnEps); |
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|
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myMinimizer->minimize(problem, endCriteria); |
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|
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delete myMinimizer; |
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} else if (simParams->haveEnsemble()) { |
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//create Integrator |
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|
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Integrator* myIntegrator = IntegratorFactory::getInstance()->createIntegrator(toUpperCopy(simParams->getEnsemble()), info); |
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|
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if (myIntegrator == NULL) { |
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sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n", |
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simParams->getEnsemble().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//Thermodynamic Integration Method |
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//set the force manager for thermodynamic integration if specified |
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if (simParams->getUseThermodynamicIntegration()){ |
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ForceManager* fman = new ThermoIntegrationForceManager(info); |
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myIntegrator->setForceManager(fman); |
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} |
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|
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// Restraints |
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if (simParams->getUseRestraints() && !simParams->getUseThermodynamicIntegration()) { |
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ForceManager* fman = new RestraintForceManager(info); |
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myIntegrator->setForceManager(fman); |
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} |
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|
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//Zconstraint-Method |
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if (simParams->getNZconsStamps() > 0) { |
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info->setNZconstraint(simParams->getNZconsStamps()); |
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ForceManager* fman = new ZconstraintForceManager(info); |
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myIntegrator->setForceManager(fman); |
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} |
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|
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myIntegrator->integrate(); |
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delete myIntegrator; |
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}else { |
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sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n", |
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simParams->getEnsemble().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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delete info; |
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|
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|
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strcpy( checkPointMsg, "Great googly moogly! It worked!" ); |
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errorCheckPoint(); |
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|
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#ifdef IS_MPI |
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MPI_Finalize(); |
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#endif |
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|
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return 0 ; |
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} |
