| 1 |
gezelter |
1390 |
/* |
| 2 |
gezelter |
1406 |
* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved. |
| 3 |
gezelter |
1390 |
* |
| 4 |
|
|
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
|
|
* non-exclusive, royalty free, license to use, modify and |
| 6 |
|
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
|
* that the following conditions are met: |
| 8 |
|
|
* |
| 9 |
|
|
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
|
* |
| 12 |
|
|
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
|
* documentation and/or other materials provided with the |
| 15 |
|
|
* distribution. |
| 16 |
|
|
* |
| 17 |
|
|
* This software is provided "AS IS," without a warranty of any |
| 18 |
|
|
* kind. All express or implied conditions, representations and |
| 19 |
|
|
* warranties, including any implied warranty of merchantability, |
| 20 |
|
|
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
|
|
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
|
|
* be liable for any damages suffered by licensee as a result of |
| 23 |
|
|
* using, modifying or distributing the software or its |
| 24 |
|
|
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
|
|
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
|
|
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
|
|
* damages, however caused and regardless of the theory of liability, |
| 28 |
|
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
|
* such damages. |
| 31 |
|
|
* |
| 32 |
|
|
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
|
|
* research, please cite the appropriate papers when you publish your |
| 34 |
|
|
* work. Good starting points are: |
| 35 |
|
|
* |
| 36 |
|
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
gezelter |
1665 |
* [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 |
gezelter |
1746 |
* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |
| 42 |
gezelter |
1390 |
*/ |
| 43 |
|
|
|
| 44 |
|
|
#ifdef IS_MPI |
| 45 |
|
|
#include <mpi.h> |
| 46 |
|
|
#endif |
| 47 |
|
|
|
| 48 |
|
|
#include <fstream> |
| 49 |
|
|
#include "utils/simError.h" |
| 50 |
|
|
#include "utils/CaseConversion.hpp" |
| 51 |
|
|
#include "brains/Register.hpp" |
| 52 |
|
|
#include "brains/SimCreator.hpp" |
| 53 |
|
|
#include "brains/SimInfo.hpp" |
| 54 |
|
|
#include "constraints/ZconstraintForceManager.hpp" |
| 55 |
|
|
#include "restraints/RestraintForceManager.hpp" |
| 56 |
|
|
#include "integrators/IntegratorFactory.hpp" |
| 57 |
|
|
#include "integrators/Integrator.hpp" |
| 58 |
gezelter |
1744 |
#include "optimization/OptimizationFactory.hpp" |
| 59 |
|
|
#include "optimization/Method.hpp" |
| 60 |
|
|
#include "optimization/Constraint.hpp" |
| 61 |
|
|
#include "optimization/Problem.hpp" |
| 62 |
|
|
#include "optimization/PotentialEnergyObjectiveFunction.hpp" |
| 63 |
gezelter |
1390 |
#include "restraints/ThermoIntegrationForceManager.hpp" |
| 64 |
|
|
|
| 65 |
|
|
using namespace OpenMD; |
| 66 |
gezelter |
1744 |
using namespace QuantLib; |
| 67 |
gezelter |
1390 |
|
| 68 |
|
|
int main(int argc,char* argv[]){ |
| 69 |
|
|
|
| 70 |
|
|
// first things first, all of the initializations |
| 71 |
|
|
|
| 72 |
|
|
#ifdef IS_MPI |
| 73 |
|
|
MPI_Init( &argc, &argv ); // the MPI communicators |
| 74 |
|
|
#endif |
| 75 |
|
|
|
| 76 |
|
|
initSimError(); // the error handler |
| 77 |
gezelter |
1767 |
//srand48( 1337 ); // the random number generator. |
| 78 |
gezelter |
1461 |
|
| 79 |
gezelter |
1463 |
std::string svnrev; |
| 80 |
gezelter |
1461 |
//convert a macro from compiler to a string in c++ |
| 81 |
gezelter |
1463 |
STR_DEFINE(svnrev, SVN_REV ); |
| 82 |
gezelter |
1462 |
|
| 83 |
gezelter |
1463 |
std::string revision; |
| 84 |
gezelter |
1461 |
|
| 85 |
gezelter |
1463 |
if (!svnrev.empty()) { |
| 86 |
|
|
revision.assign(" Revision: " + svnrev); |
| 87 |
|
|
} |
| 88 |
|
|
|
| 89 |
|
|
revision.resize(19,' '); |
| 90 |
|
|
|
| 91 |
gezelter |
1390 |
#ifdef IS_MPI |
| 92 |
|
|
if( worldRank == 0 ){ |
| 93 |
|
|
#endif |
| 94 |
|
|
std::cerr << |
| 95 |
gezelter |
1665 |
" +--------------------------------------------------------------------------+\n"<< |
| 96 |
|
|
" | ____ __ ___ ____ |\n"<< |
| 97 |
|
|
" | / __ \\____ ___ ____ / |/ // __ \\ The Open Molecular Dynamics |\n"<< |
| 98 |
|
|
" | / / / / __ \\/ _ \\/ __ \\ / /|_/ // / / / Engine (formerly OOPSE). |\n"<< |
| 99 |
|
|
" | / /_/ / /_/ / __/ / / // / / // /_/ / |\n"<< |
| 100 |
gezelter |
1695 |
" | \\____/ .___/\\___/_/ /_//_/ /_//_____/ Copyright 2004-2012 by the |\n"<< |
| 101 |
gezelter |
1665 |
" | /_/ University of Notre Dame. |\n"<< |
| 102 |
|
|
" | |\n"<< |
| 103 |
gezelter |
1461 |
" | version " << |
| 104 |
gezelter |
1463 |
OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << revision << |
| 105 |
gezelter |
1665 |
" http://www.openmd.net |\n"<< |
| 106 |
|
|
" | |\n"<< |
| 107 |
|
|
" | OpenMD is an OpenScience project. All source code is available for any |\n"<< |
| 108 |
|
|
" | use whatsoever under a BSD-style license. |\n"<< |
| 109 |
|
|
" | |\n"<< |
| 110 |
|
|
" | Support OpenScience! If you use OpenMD or its source code in your |\n"<< |
| 111 |
|
|
" | research, please cite the appropriate papers when you publish your work |\n"<< |
| 112 |
|
|
" | Good starting points are: |\n"<< |
| 113 |
|
|
" | |\n"<< |
| 114 |
|
|
" | [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |\n"<< |
| 115 |
|
|
" | [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |\n"<< |
| 116 |
|
|
" | [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |\n"<< |
| 117 |
|
|
" | [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |\n"<< |
| 118 |
|
|
" | [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |\n"<< |
| 119 |
gezelter |
1746 |
" | [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012). |\n"<< |
| 120 |
gezelter |
1665 |
" +--------------------------------------------------------------------------+\n"<< |
| 121 |
gezelter |
1390 |
"\n"; |
| 122 |
|
|
|
| 123 |
|
|
if( argc < 2 ){ |
| 124 |
|
|
strcpy( painCave.errMsg, "Error, a meta-data file is needed to run.\n" ); |
| 125 |
|
|
painCave.isFatal = 1; |
| 126 |
|
|
simError(); |
| 127 |
|
|
} |
| 128 |
|
|
#ifdef IS_MPI |
| 129 |
|
|
} |
| 130 |
|
|
#endif |
| 131 |
|
|
|
| 132 |
|
|
strcpy( checkPointMsg, "Successful number of arguments" ); |
| 133 |
|
|
errorCheckPoint(); |
| 134 |
|
|
|
| 135 |
|
|
//register forcefields, integrators and minimizers |
| 136 |
|
|
registerAll(); |
| 137 |
|
|
|
| 138 |
|
|
//create simulation model |
| 139 |
|
|
SimCreator creator; |
| 140 |
|
|
SimInfo* info = creator.createSim(argv[1]); |
| 141 |
gezelter |
1540 |
|
| 142 |
gezelter |
1390 |
Globals* simParams = info->getSimParams(); |
| 143 |
gezelter |
1746 |
MinimizerParameters* miniPars = simParams->getMinimizerParameters(); |
| 144 |
gezelter |
1390 |
|
| 145 |
gezelter |
1747 |
if (miniPars->getUseMinimizer() && simParams->haveEnsemble()) { |
| 146 |
gezelter |
1746 |
sprintf(painCave.errMsg, "Ensemble keyword can not co-exist with useMinimizer = \"true\" in the minimizer block\n"); |
| 147 |
gezelter |
1390 |
painCave.isFatal = 1; |
| 148 |
|
|
simError(); |
| 149 |
|
|
} |
| 150 |
chuckv |
1496 |
|
| 151 |
gezelter |
1747 |
if (miniPars->getUseMinimizer()) { |
| 152 |
gezelter |
1390 |
//create minimizer |
| 153 |
gezelter |
1746 |
OptimizationMethod* myMinimizer =OptimizationFactory::getInstance()->createOptimization(toUpperCopy(miniPars->getMethod()), info); |
| 154 |
gezelter |
1390 |
|
| 155 |
|
|
if (myMinimizer == NULL) { |
| 156 |
gezelter |
1744 |
sprintf(painCave.errMsg, "Optimization Factory can not create %s OptimizationMethod\n", |
| 157 |
gezelter |
1746 |
miniPars->getMethod().c_str()); |
| 158 |
gezelter |
1390 |
painCave.isFatal = 1; |
| 159 |
|
|
simError(); |
| 160 |
|
|
} |
| 161 |
|
|
|
| 162 |
gezelter |
1744 |
ForceManager* fman = new ForceManager(info); |
| 163 |
|
|
fman->initialize(); |
| 164 |
|
|
|
| 165 |
|
|
PotentialEnergyObjectiveFunction potObjf(info, fman); |
| 166 |
|
|
DumpStatusFunction dsf(info); |
| 167 |
|
|
DynamicVector<RealType> initCoords = potObjf.setInitialCoords(); |
| 168 |
|
|
Problem problem(potObjf, *(new NoConstraint()), dsf, initCoords); |
| 169 |
|
|
|
| 170 |
gezelter |
1746 |
|
| 171 |
|
|
int maxIter = miniPars->getMaxIterations(); |
| 172 |
|
|
int mssIter = miniPars->getMaxStationaryStateIterations(); |
| 173 |
|
|
RealType rEps = miniPars->getRootEpsilon(); |
| 174 |
|
|
RealType fEps = miniPars->getFunctionEpsilon(); |
| 175 |
|
|
RealType gnEps = miniPars->getGradientNormEpsilon(); |
| 176 |
|
|
|
| 177 |
|
|
EndCriteria endCriteria(maxIter, mssIter, rEps, fEps, gnEps); |
| 178 |
|
|
|
| 179 |
gezelter |
1744 |
myMinimizer->minimize(problem, endCriteria); |
| 180 |
|
|
|
| 181 |
gezelter |
1390 |
delete myMinimizer; |
| 182 |
|
|
} else if (simParams->haveEnsemble()) { |
| 183 |
|
|
//create Integrator |
| 184 |
|
|
|
| 185 |
|
|
Integrator* myIntegrator = IntegratorFactory::getInstance()->createIntegrator(toUpperCopy(simParams->getEnsemble()), info); |
| 186 |
|
|
|
| 187 |
|
|
if (myIntegrator == NULL) { |
| 188 |
|
|
sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n", |
| 189 |
|
|
simParams->getEnsemble().c_str()); |
| 190 |
|
|
painCave.isFatal = 1; |
| 191 |
|
|
simError(); |
| 192 |
|
|
} |
| 193 |
|
|
|
| 194 |
|
|
//Thermodynamic Integration Method |
| 195 |
|
|
//set the force manager for thermodynamic integration if specified |
| 196 |
|
|
if (simParams->getUseThermodynamicIntegration()){ |
| 197 |
|
|
ForceManager* fman = new ThermoIntegrationForceManager(info); |
| 198 |
|
|
myIntegrator->setForceManager(fman); |
| 199 |
|
|
} |
| 200 |
|
|
|
| 201 |
|
|
// Restraints |
| 202 |
|
|
if (simParams->getUseRestraints() && !simParams->getUseThermodynamicIntegration()) { |
| 203 |
|
|
ForceManager* fman = new RestraintForceManager(info); |
| 204 |
|
|
myIntegrator->setForceManager(fman); |
| 205 |
|
|
} |
| 206 |
|
|
|
| 207 |
|
|
//Zconstraint-Method |
| 208 |
|
|
if (simParams->getNZconsStamps() > 0) { |
| 209 |
|
|
info->setNZconstraint(simParams->getNZconsStamps()); |
| 210 |
|
|
ForceManager* fman = new ZconstraintForceManager(info); |
| 211 |
|
|
myIntegrator->setForceManager(fman); |
| 212 |
|
|
} |
| 213 |
|
|
|
| 214 |
|
|
myIntegrator->integrate(); |
| 215 |
|
|
delete myIntegrator; |
| 216 |
|
|
}else { |
| 217 |
|
|
sprintf(painCave.errMsg, "Integrator Factory can not create %s Integrator\n", |
| 218 |
|
|
simParams->getEnsemble().c_str()); |
| 219 |
|
|
painCave.isFatal = 1; |
| 220 |
|
|
simError(); |
| 221 |
|
|
} |
| 222 |
|
|
|
| 223 |
|
|
delete info; |
| 224 |
|
|
|
| 225 |
|
|
|
| 226 |
|
|
strcpy( checkPointMsg, "Great googly moogly! It worked!" ); |
| 227 |
|
|
errorCheckPoint(); |
| 228 |
|
|
|
| 229 |
|
|
#ifdef IS_MPI |
| 230 |
|
|
MPI_Finalize(); |
| 231 |
|
|
#endif |
| 232 |
|
|
|
| 233 |
|
|
return 0 ; |
| 234 |
|
|
} |
