| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2010). |
| 40 |
< |
* $Revision$ |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
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|
| 43 |
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#ifdef IS_MPI |
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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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– |
|
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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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initSimError(); // the error handler |
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srand48( 1337 ); // the random number generator. |
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< |
|
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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 |
| 91 |
|
if( worldRank == 0 ){ |
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|
#endif |
| 93 |
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std::cerr << |
| 94 |
< |
" +-----------------------------------------------------------------------+\n"<< |
| 95 |
< |
" | ____ __ ___ ____ |\n"<< |
| 96 |
< |
" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
| 97 |
< |
" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
| 98 |
< |
" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
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< |
" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2010 by the |\n"<< |
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< |
" | /_/ University of Notre Dame. |\n"<< |
| 101 |
< |
" | |\n"<< |
| 102 |
< |
" | version " << |
| 103 |
< |
OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << " Rev:" << __get_svn_version() << |
| 104 |
< |
" http://www.openmd.net |\n"<< |
| 105 |
< |
" | |\n"<< |
| 106 |
< |
" | OpenMD is an OpenScience project. All source code is available for |\n"<< |
| 107 |
< |
" | any use whatsoever under a BSD-style license. |\n"<< |
| 108 |
< |
" | |\n"<< |
| 109 |
< |
" | Support OpenScience! If you use OpenMD or its source code in your |\n"<< |
| 110 |
< |
" | research, please cite the appropriate papers when you publish your |\n"<< |
| 111 |
< |
" | work. Good starting points are: |\n"<< |
| 112 |
< |
" | |\n"<< |
| 113 |
< |
" | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n"<< |
| 114 |
< |
" | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n"<< |
| 115 |
< |
" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |\n"<< |
| 116 |
< |
" | [4] Vardeman & Gezelter, in progress (2010). |\n"<< |
| 117 |
< |
" +-----------------------------------------------------------------------+\n"<< |
| 94 |
> |
" +--------------------------------------------------------------------------+\n"<< |
| 95 |
> |
" | ____ __ ___ ____ |\n"<< |
| 96 |
> |
" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
| 97 |
> |
" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
| 98 |
> |
" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
| 99 |
> |
" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2012 by the |\n"<< |
| 100 |
> |
" | /_/ University of Notre Dame. |\n"<< |
| 101 |
> |
" | |\n"<< |
| 102 |
> |
" | version " << |
| 103 |
> |
OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << revision << |
| 104 |
> |
" http://www.openmd.net |\n"<< |
| 105 |
> |
" | |\n"<< |
| 106 |
> |
" | OpenMD is an OpenScience project. All source code is available for any |\n"<< |
| 107 |
> |
" | use whatsoever under a BSD-style license. |\n"<< |
| 108 |
> |
" | |\n"<< |
| 109 |
> |
" | Support OpenScience! If you use OpenMD or its source code in your |\n"<< |
| 110 |
> |
" | research, please cite the appropriate papers when you publish your work |\n"<< |
| 111 |
> |
" | Good starting points are: |\n"<< |
| 112 |
> |
" | |\n"<< |
| 113 |
> |
" | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n"<< |
| 114 |
> |
" | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n"<< |
| 115 |
> |
" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |\n"<< |
| 116 |
> |
" | [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |\n"<< |
| 117 |
> |
" | [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n"<< |
| 118 |
> |
" | [6] Kuang & Gezelter, Mol. Phys., in press (2012). |\n"<< |
| 119 |
> |
" +--------------------------------------------------------------------------+\n"<< |
| 120 |
|
"\n"; |
| 121 |
|
|
| 122 |
|
if( argc < 2 ){ |
| 137 |
|
//create simulation model |
| 138 |
|
SimCreator creator; |
| 139 |
|
SimInfo* info = creator.createSim(argv[1]); |
| 140 |
+ |
|
| 141 |
|
Globals* simParams = info->getSimParams(); |
| 142 |
|
|
| 143 |
|
if (simParams->haveMinimizer() && simParams->haveEnsemble()) { |
| 145 |
|
painCave.isFatal = 1; |
| 146 |
|
simError(); |
| 147 |
|
} |
| 148 |
< |
|
| 148 |
> |
|
| 149 |
> |
|
| 150 |
|
if (simParams->haveMinimizer()) { |
| 151 |
|
//create minimizer |
| 152 |
< |
Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info); |
| 152 |
> |
OptimizationMethod* myMinimizer =OptimizationFactory::getInstance()->createOptimization(toUpperCopy(simParams->getMinimizer()), info); |
| 153 |
|
|
| 154 |
|
if (myMinimizer == NULL) { |
| 155 |
< |
sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n", |
| 155 |
> |
sprintf(painCave.errMsg, "Optimization Factory can not create %s OptimizationMethod\n", |
| 156 |
|
simParams->getMinimizer().c_str()); |
| 157 |
|
painCave.isFatal = 1; |
| 158 |
|
simError(); |
| 159 |
|
} |
| 160 |
|
|
| 161 |
< |
myMinimizer->minimize(); |
| 161 |
> |
ForceManager* fman = new ForceManager(info); |
| 162 |
> |
fman->initialize(); |
| 163 |
> |
|
| 164 |
> |
PotentialEnergyObjectiveFunction potObjf(info, fman); |
| 165 |
> |
DumpStatusFunction dsf(info); |
| 166 |
> |
DynamicVector<RealType> initCoords = potObjf.setInitialCoords(); |
| 167 |
> |
Problem problem(potObjf, *(new NoConstraint()), dsf, initCoords); |
| 168 |
> |
EndCriteria endCriteria(1000, 100, 1e-5, 1e-5, 1e-5); |
| 169 |
> |
|
| 170 |
> |
myMinimizer->minimize(problem, endCriteria); |
| 171 |
> |
|
| 172 |
|
delete myMinimizer; |
| 173 |
|
} else if (simParams->haveEnsemble()) { |
| 174 |
|
//create Integrator |
| 223 |
|
|
| 224 |
|
return 0 ; |
| 225 |
|
} |
| 197 |
– |
|
| 198 |
– |
extern "C" { |
| 199 |
– |
|
| 200 |
– |
char svnVersionString[1024]; |
| 201 |
– |
char* __get_svn_version(){ |
| 202 |
– |
int howMuchToCopy=0; |
| 203 |
– |
char *theVersion="$Revision$"; |
| 204 |
– |
howMuchToCopy=strlen(theVersion+11) - 2; |
| 205 |
– |
assert(howMuchToCopy>0); |
| 206 |
– |
memcpy(svnVersionString, theVersion+11, howMuchToCopy); |
| 207 |
– |
svnVersionString[howMuchToCopy] = '\0'; |
| 208 |
– |
return svnVersionString; |
| 209 |
– |
} |
| 210 |
– |
|
| 211 |
– |
} |
