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#include <iostream> |
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#include <fstream> |
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#include <cstdlib> |
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#include <cmath> |
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#include <cstring> |
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|
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/* |
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* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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#ifdef PROFILE |
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#include "profiling/mdProfile.hpp" |
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#endif // PROFILE |
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#include <fstream> |
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#include "utils/simError.h" |
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#include "brains/SimSetup.hpp" |
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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 "primitives/Atom.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 "brains/Thermo.hpp" |
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#include "io/ReadWrite.hpp" |
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#include "minimizers/OOPSEMinimizer.hpp" |
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#include "minimizers/MinimizerFactory.hpp" |
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#include "minimizers/Minimizer.hpp" |
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#include "restraints/ThermoIntegrationForceManager.hpp" |
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char* program_name; |
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using namespace std; |
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using namespace oopse; |
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int main(int argc,char* argv[]){ |
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char* in_name; |
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SimSetup* startMe; |
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SimInfo* entry_plug; |
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// first things first, all of the initializations |
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#ifdef IS_MPI |
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initSimError(); // the error handler |
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srand48( 1337 ); // the random number generator. |
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#ifdef PROFILE |
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initProfile(); |
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#endif //profile |
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// check command line arguments, and set the input file |
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program_name = argv[0]; // save the program name in case we need it |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
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" | ____ ____ ____ _____ ______ The OpenSource, Object-oriented |\n" << |
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" | / __ \\/ __ \\/ __ \\/ ___// ____/ Parallel Simulation Engine. |\n" << |
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" | / / / / / / / /_/ /\\__ \\/ __/ |\n" << |
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" | / /_/ / /_/ / ____/___/ / /___ Copyright 2004 by the |\n" << |
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" | / /_/ / /_/ / ____/___/ / /___ Copyright 2004-2008 by the |\n" << |
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" | \\____/\\____/_/ /____/_____/ University of Notre Dame. |\n" << |
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" | http://www.oopse.org |\n" << |
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" | |\n" << |
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" | version " << |
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OOPSE_VERSION_MAJOR << "." << OOPSE_VERSION_MINOR << "." << OOPSE_VERSION_TINY << |
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" http://www.oopse.org |\n" << |
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" | |\n" << |
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" | OOPSE is an OpenScience project. All source code is available for |\n" << |
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" | any use subject to only one condition: |\n" << |
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" | |\n" << |
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" | Any published work resulting from the use of this code must cite the |\n" << |
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" | following paper: M. A. Meineke, C. F. Vardeman II, T. Lin, |\n" << |
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" | C. J. Fennell, and J. D. Gezelter, |\n" << |
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" | J. Comp. Chem. XX, XXXX (2004). |\n" << |
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" | J. Comput. Chem. 26, pp. 252-271 (2005). |\n" << |
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" +----------------------------------------------------------------------+\n" << |
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"\n"; |
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} |
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#endif |
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in_name = argv[1]; |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Successful number of arguments" ); |
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MPIcheckPoint(); |
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#endif |
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// create the simulation objects, and get the show on the road |
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errorCheckPoint(); |
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entry_plug = new SimInfo(); |
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startMe = new SimSetup(); |
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//register forcefields, integrators and minimizers |
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registerAll(); |
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startMe->setSimInfo( entry_plug ); |
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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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Globals* simParams = info->getSimParams(); |
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#ifdef PROFILE |
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startProfile( pro1 ); |
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#endif //profile |
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if (simParams->haveMinimizer() && simParams->haveEnsemble()) { |
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sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\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 (simParams->haveMinimizer()) { |
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//create minimizer |
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Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info); |
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startMe->parseFile( in_name ); |
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if (myMinimizer == NULL) { |
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sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n", |
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simParams->getMinimizer().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef PROFILE |
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endProfile( pro1 ); |
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startProfile( pro2 ); |
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#endif //profile |
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myMinimizer->minimize(); |
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delete myMinimizer; |
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} else if (simParams->haveEnsemble()) { |
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//create Integrator |
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startMe->createSim(); |
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delete startMe; |
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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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#ifdef PROFILE |
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endProfile( pro2 ); |
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startProfile( pro3 ); |
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#endif //profile |
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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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if (!entry_plug->has_minimizer) |
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entry_plug->the_integrator->integrate(); |
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else |
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entry_plug->the_minimizer->minimize(); |
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#ifdef PROFILE |
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endProfile( pro3 ); |
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|
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writeProfiles(); |
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#endif //profile |
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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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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Oh what a lovely Tea Party!" ); |
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MPIcheckPoint(); |
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|
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MPI_Finalize(); |
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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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return 0 ; |
