| 38 |
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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). |
| 41 |
+ |
* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |
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*/ |
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#ifdef IS_MPI |
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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 "restraints/RestraintForceManager.hpp" |
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#include "integrators/IntegratorFactory.hpp" |
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#include "integrators/Integrator.hpp" |
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< |
#include "minimizers/MinimizerFactory.hpp" |
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< |
#include "minimizers/Minimizer.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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#endif |
| 77 |
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|
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initSimError(); // the error handler |
| 79 |
< |
srand48( 1337 ); // the random number generator. |
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> |
//srand48( 1337 ); // the random number generator. |
| 80 |
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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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" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
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" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
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" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
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< |
" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2011 by the |\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"<< |
| 105 |
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" | version " << |
| 118 |
|
" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |\n"<< |
| 119 |
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" | [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |\n"<< |
| 120 |
|
" | [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n"<< |
| 121 |
+ |
" | [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |\n"<< |
| 122 |
|
" +--------------------------------------------------------------------------+\n"<< |
| 123 |
|
"\n"; |
| 124 |
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|
| 142 |
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SimInfo* info = creator.createSim(argv[1]); |
| 143 |
|
|
| 144 |
|
Globals* simParams = info->getSimParams(); |
| 145 |
+ |
MinimizerParameters* miniPars = simParams->getMinimizerParameters(); |
| 146 |
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|
| 147 |
< |
if (simParams->haveMinimizer() && simParams->haveEnsemble()) { |
| 148 |
< |
sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\n"); |
| 147 |
> |
if (miniPars->getUseMinimizer() && simParams->haveEnsemble()) { |
| 148 |
> |
sprintf(painCave.errMsg, "Ensemble keyword can not co-exist with useMinimizer = \"true\" in the minimizer block\n"); |
| 149 |
|
painCave.isFatal = 1; |
| 150 |
|
simError(); |
| 151 |
|
} |
| 143 |
– |
|
| 152 |
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|
| 153 |
< |
if (simParams->haveMinimizer()) { |
| 153 |
> |
if (miniPars->getUseMinimizer()) { |
| 154 |
|
//create minimizer |
| 155 |
< |
Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info); |
| 155 |
> |
OptimizationMethod* myMinimizer =OptimizationFactory::getInstance()->createOptimization(toUpperCopy(miniPars->getMethod()), info); |
| 156 |
|
|
| 157 |
|
if (myMinimizer == NULL) { |
| 158 |
< |
sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n", |
| 159 |
< |
simParams->getMinimizer().c_str()); |
| 158 |
> |
sprintf(painCave.errMsg, "Optimization Factory can not create %s OptimizationMethod\n", |
| 159 |
> |
miniPars->getMethod().c_str()); |
| 160 |
|
painCave.isFatal = 1; |
| 161 |
|
simError(); |
| 162 |
|
} |
| 163 |
|
|
| 164 |
< |
myMinimizer->minimize(); |
| 164 |
> |
ForceManager* fman = new ForceManager(info); |
| 165 |
> |
fman->initialize(); |
| 166 |
> |
|
| 167 |
> |
PotentialEnergyObjectiveFunction potObjf(info, fman); |
| 168 |
> |
DumpStatusFunction dsf(info); |
| 169 |
> |
DynamicVector<RealType> initCoords = potObjf.setInitialCoords(); |
| 170 |
> |
Problem problem(potObjf, *(new NoConstraint()), dsf, initCoords); |
| 171 |
> |
|
| 172 |
> |
|
| 173 |
> |
int maxIter = miniPars->getMaxIterations(); |
| 174 |
> |
int mssIter = miniPars->getMaxStationaryStateIterations(); |
| 175 |
> |
RealType rEps = miniPars->getRootEpsilon(); |
| 176 |
> |
RealType fEps = miniPars->getFunctionEpsilon(); |
| 177 |
> |
RealType gnEps = miniPars->getGradientNormEpsilon(); |
| 178 |
> |
|
| 179 |
> |
EndCriteria endCriteria(maxIter, mssIter, rEps, fEps, gnEps); |
| 180 |
> |
|
| 181 |
> |
myMinimizer->minimize(problem, endCriteria); |
| 182 |
> |
|
| 183 |
|
delete myMinimizer; |
| 184 |
|
} else if (simParams->haveEnsemble()) { |
| 185 |
|
//create Integrator |
