| 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 |
< |
* $Revision$ |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
> |
* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |
| 42 |
|
*/ |
| 43 |
|
|
| 44 |
|
#ifdef IS_MPI |
| 46 |
|
#endif |
| 47 |
|
|
| 48 |
|
#include <fstream> |
| 49 |
+ |
#include <iostream> |
| 50 |
+ |
#include <locale> |
| 51 |
|
#include "utils/simError.h" |
| 52 |
|
#include "utils/CaseConversion.hpp" |
| 53 |
+ |
#include "utils/Revision.hpp" |
| 54 |
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#include "brains/Register.hpp" |
| 55 |
|
#include "brains/SimCreator.hpp" |
| 56 |
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#include "brains/SimInfo.hpp" |
| 58 |
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#include "restraints/RestraintForceManager.hpp" |
| 59 |
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#include "integrators/IntegratorFactory.hpp" |
| 60 |
|
#include "integrators/Integrator.hpp" |
| 61 |
< |
#include "minimizers/MinimizerFactory.hpp" |
| 62 |
< |
#include "minimizers/Minimizer.hpp" |
| 61 |
> |
#include "optimization/OptimizationFactory.hpp" |
| 62 |
> |
#include "optimization/Method.hpp" |
| 63 |
> |
#include "optimization/Constraint.hpp" |
| 64 |
> |
#include "optimization/Problem.hpp" |
| 65 |
> |
#include "optimization/PotentialEnergyObjectiveFunction.hpp" |
| 66 |
|
#include "restraints/ThermoIntegrationForceManager.hpp" |
| 67 |
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|
| 68 |
|
using namespace OpenMD; |
| 69 |
+ |
using namespace QuantLib; |
| 70 |
|
|
| 71 |
< |
|
| 64 |
< |
int main(int argc,char* argv[]){ |
| 71 |
> |
int main(int argc, char* argv[]){ |
| 72 |
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|
| 73 |
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// first things first, all of the initializations |
| 74 |
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|
| 77 |
|
#endif |
| 78 |
|
|
| 79 |
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initSimError(); // the error handler |
| 80 |
< |
srand48( 1337 ); // the random number generator. |
| 81 |
< |
|
| 80 |
> |
//srand48( 1337 ); // the random number generator. |
| 81 |
> |
|
| 82 |
> |
std::string svnrev(g_REVISION, strnlen(g_REVISION, 20)); |
| 83 |
> |
//convert a macro from compiler to a string in c++ |
| 84 |
> |
//STR_DEFINE(svnrev, SVN_REV ); |
| 85 |
> |
|
| 86 |
> |
std::string revision; |
| 87 |
> |
|
| 88 |
> |
if (!svnrev.empty()) { |
| 89 |
> |
revision.assign(" Revision: " + svnrev); |
| 90 |
> |
} |
| 91 |
> |
|
| 92 |
> |
revision.resize(19,' '); |
| 93 |
> |
|
| 94 |
|
#ifdef IS_MPI |
| 95 |
|
if( worldRank == 0 ){ |
| 96 |
|
#endif |
| 97 |
|
std::cerr << |
| 98 |
< |
" +-----------------------------------------------------------------------+\n"<< |
| 99 |
< |
" | ____ __ ___ ____ |\n"<< |
| 100 |
< |
" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
| 101 |
< |
" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
| 102 |
< |
" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
| 103 |
< |
" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2010 by the |\n"<< |
| 104 |
< |
" | /_/ University of Notre Dame. |\n"<< |
| 105 |
< |
" | |\n"<< |
| 106 |
< |
" | version " << |
| 107 |
< |
OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << " Rev:" << __get_svn_version() << |
| 108 |
< |
" http://www.openmd.net |\n"<< |
| 109 |
< |
" | |\n"<< |
| 110 |
< |
" | OpenMD is an OpenScience project. All source code is available for |\n"<< |
| 111 |
< |
" | any use whatsoever under a BSD-style license. |\n"<< |
| 112 |
< |
" | |\n"<< |
| 113 |
< |
" | Support OpenScience! If you use OpenMD or its source code in your |\n"<< |
| 114 |
< |
" | research, please cite the appropriate papers when you publish your |\n"<< |
| 115 |
< |
" | work. Good starting points are: |\n"<< |
| 116 |
< |
" | |\n"<< |
| 117 |
< |
" | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n"<< |
| 118 |
< |
" | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n"<< |
| 119 |
< |
" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |\n"<< |
| 120 |
< |
" | [4] Vardeman & Gezelter, in progress (2010). |\n"<< |
| 121 |
< |
" +-----------------------------------------------------------------------+\n"<< |
| 98 |
> |
" +--------------------------------------------------------------------------+\n"<< |
| 99 |
> |
" | ____ __ ___ ____ |\n"<< |
| 100 |
> |
" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
| 101 |
> |
" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
| 102 |
> |
" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
| 103 |
> |
" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2015 by the |\n"<< |
| 104 |
> |
" | /_/ University of Notre Dame. |\n"<< |
| 105 |
> |
" | |\n"<< |
| 106 |
> |
" | version " << |
| 107 |
> |
OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << revision << |
| 108 |
> |
" http://www.openmd.org |\n"<< |
| 109 |
> |
" | |\n"<< |
| 110 |
> |
" | OpenMD is an OpenScience project. All source code is available for any |\n"<< |
| 111 |
> |
" | use whatsoever under a BSD-style license. |\n"<< |
| 112 |
> |
" | |\n"<< |
| 113 |
> |
" | Support OpenScience! If you use OpenMD or its source code in your |\n"<< |
| 114 |
> |
" | research, please cite the appropriate papers when you publish your work. |\n"<< |
| 115 |
> |
" | Good starting points for code and simulation methodology are: |\n"<< |
| 116 |
> |
" | |\n"<< |
| 117 |
> |
" | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n"<< |
| 118 |
> |
" | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n"<< |
| 119 |
> |
" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |\n"<< |
| 120 |
> |
" | [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n"<< |
| 121 |
> |
" | [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |\n"<< |
| 122 |
> |
" | [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141 134109 (2014). |\n"<< |
| 123 |
> |
" | [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141 134110 (2014). |\n"<< |
| 124 |
> |
" +--------------------------------------------------------------------------+\n"<< |
| 125 |
|
"\n"; |
| 126 |
|
|
| 127 |
|
if( argc < 2 ){ |
| 142 |
|
//create simulation model |
| 143 |
|
SimCreator creator; |
| 144 |
|
SimInfo* info = creator.createSim(argv[1]); |
| 145 |
+ |
|
| 146 |
|
Globals* simParams = info->getSimParams(); |
| 147 |
+ |
MinimizerParameters* miniPars = simParams->getMinimizerParameters(); |
| 148 |
|
|
| 149 |
< |
if (simParams->haveMinimizer() && simParams->haveEnsemble()) { |
| 150 |
< |
sprintf(painCave.errMsg, "Minimizer keyword and Ensemble keyword can not exist together\n"); |
| 149 |
> |
if (miniPars->getUseMinimizer() && simParams->haveEnsemble()) { |
| 150 |
> |
sprintf(painCave.errMsg, "Ensemble keyword can not co-exist with useMinimizer = \"true\" in the minimizer block\n"); |
| 151 |
|
painCave.isFatal = 1; |
| 152 |
|
simError(); |
| 153 |
|
} |
| 154 |
< |
|
| 155 |
< |
if (simParams->haveMinimizer()) { |
| 154 |
> |
|
| 155 |
> |
if (miniPars->getUseMinimizer()) { |
| 156 |
|
//create minimizer |
| 157 |
< |
Minimizer* myMinimizer = MinimizerFactory::getInstance()->createMinimizer(toUpperCopy(simParams->getMinimizer()), info); |
| 157 |
> |
OptimizationMethod* myMinimizer =OptimizationFactory::getInstance()->createOptimization(toUpperCopy(miniPars->getMethod()), info); |
| 158 |
|
|
| 159 |
|
if (myMinimizer == NULL) { |
| 160 |
< |
sprintf(painCave.errMsg, "Minimizer Factory can not create %s Minimizer\n", |
| 161 |
< |
simParams->getMinimizer().c_str()); |
| 160 |
> |
sprintf(painCave.errMsg, "Optimization Factory can not create %s OptimizationMethod\n", |
| 161 |
> |
miniPars->getMethod().c_str()); |
| 162 |
|
painCave.isFatal = 1; |
| 163 |
|
simError(); |
| 164 |
|
} |
| 165 |
|
|
| 166 |
< |
myMinimizer->minimize(); |
| 166 |
> |
ForceManager* fman = new ForceManager(info); |
| 167 |
> |
fman->initialize(); |
| 168 |
> |
|
| 169 |
> |
PotentialEnergyObjectiveFunction potObjf(info, fman); |
| 170 |
> |
DumpStatusFunction dsf(info); |
| 171 |
> |
DynamicVector<RealType> initCoords = potObjf.setInitialCoords(); |
| 172 |
> |
Problem problem(potObjf, *(new NoConstraint()), dsf, initCoords); |
| 173 |
> |
|
| 174 |
> |
|
| 175 |
> |
int maxIter = miniPars->getMaxIterations(); |
| 176 |
> |
int mssIter = miniPars->getMaxStationaryStateIterations(); |
| 177 |
> |
RealType rEps = miniPars->getRootEpsilon(); |
| 178 |
> |
RealType fEps = miniPars->getFunctionEpsilon(); |
| 179 |
> |
RealType gnEps = miniPars->getGradientNormEpsilon(); |
| 180 |
> |
|
| 181 |
> |
EndCriteria endCriteria(maxIter, mssIter, rEps, fEps, gnEps); |
| 182 |
> |
|
| 183 |
> |
myMinimizer->minimize(problem, endCriteria); |
| 184 |
> |
|
| 185 |
|
delete myMinimizer; |
| 186 |
|
} else if (simParams->haveEnsemble()) { |
| 187 |
|
//create Integrator |
| 236 |
|
|
| 237 |
|
return 0 ; |
| 238 |
|
} |
| 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 |
– |
} |
