| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#ifdef IS_MPI |
| 43 |
|
#include <mpi.h> |
| 44 |
|
#endif |
| 45 |
|
|
| 46 |
+ |
#include <fstream> |
| 47 |
|
#include "utils/simError.h" |
| 48 |
|
#include "utils/CaseConversion.hpp" |
| 49 |
|
#include "brains/Register.hpp" |
| 50 |
|
#include "brains/SimCreator.hpp" |
| 51 |
|
#include "brains/SimInfo.hpp" |
| 52 |
|
#include "constraints/ZconstraintForceManager.hpp" |
| 53 |
+ |
#include "restraints/RestraintForceManager.hpp" |
| 54 |
|
#include "integrators/IntegratorFactory.hpp" |
| 55 |
|
#include "integrators/Integrator.hpp" |
| 56 |
|
#include "minimizers/MinimizerFactory.hpp" |
| 57 |
|
#include "minimizers/Minimizer.hpp" |
| 58 |
|
#include "restraints/ThermoIntegrationForceManager.hpp" |
| 59 |
|
|
| 60 |
< |
using namespace oopse; |
| 60 |
> |
using namespace OpenMD; |
| 61 |
|
|
| 62 |
+ |
|
| 63 |
|
int main(int argc,char* argv[]){ |
| 64 |
< |
|
| 64 |
> |
|
| 65 |
|
// first things first, all of the initializations |
| 66 |
|
|
| 67 |
|
#ifdef IS_MPI |
| 79 |
|
" | ____ ____ ____ _____ ______ The OpenSource, Object-oriented |\n" << |
| 80 |
|
" | / __ \\/ __ \\/ __ \\/ ___// ____/ Parallel Simulation Engine. |\n" << |
| 81 |
|
" | / / / / / / / /_/ /\\__ \\/ __/ |\n" << |
| 82 |
< |
" | / /_/ / /_/ / ____/___/ / /___ Copyright 2004-2006 by the |\n" << |
| 82 |
> |
" | / /_/ / /_/ / ____/___/ / /___ Copyright 2004-2008 by the |\n" << |
| 83 |
|
" | \\____/\\____/_/ /____/_____/ University of Notre Dame. |\n" << |
| 84 |
|
" | |\n" << |
| 85 |
|
" | version " << |
| 105 |
|
} |
| 106 |
|
#endif |
| 107 |
|
|
| 105 |
– |
#ifdef IS_MPI |
| 108 |
|
strcpy( checkPointMsg, "Successful number of arguments" ); |
| 109 |
< |
MPIcheckPoint(); |
| 108 |
< |
#endif |
| 109 |
> |
errorCheckPoint(); |
| 110 |
|
|
| 110 |
– |
|
| 111 |
– |
|
| 111 |
|
//register forcefields, integrators and minimizers |
| 112 |
|
registerAll(); |
| 113 |
|
|
| 149 |
|
|
| 150 |
|
//Thermodynamic Integration Method |
| 151 |
|
//set the force manager for thermodynamic integration if specified |
| 152 |
< |
if (simParams->getUseSolidThermInt() || simParams->getUseLiquidThermInt()){ |
| 152 |
> |
if (simParams->getUseThermodynamicIntegration()){ |
| 153 |
|
ForceManager* fman = new ThermoIntegrationForceManager(info); |
| 154 |
|
myIntegrator->setForceManager(fman); |
| 155 |
|
} |
| 156 |
|
|
| 157 |
+ |
// Restraints |
| 158 |
+ |
if (simParams->getUseRestraints() && !simParams->getUseThermodynamicIntegration()) { |
| 159 |
+ |
ForceManager* fman = new RestraintForceManager(info); |
| 160 |
+ |
myIntegrator->setForceManager(fman); |
| 161 |
+ |
} |
| 162 |
+ |
|
| 163 |
|
//Zconstraint-Method |
| 164 |
|
if (simParams->getNZconsStamps() > 0) { |
| 165 |
|
info->setNZconstraint(simParams->getNZconsStamps()); |
| 175 |
|
painCave.isFatal = 1; |
| 176 |
|
simError(); |
| 177 |
|
} |
| 173 |
– |
|
| 174 |
– |
|
| 178 |
|
|
| 179 |
|
delete info; |
| 180 |
|
|
| 181 |
< |
#ifdef IS_MPI |
| 182 |
< |
strcpy( checkPointMsg, "Yoikes! It worked!" ); |
| 183 |
< |
MPIcheckPoint(); |
| 184 |
< |
|
| 181 |
> |
|
| 182 |
> |
strcpy( checkPointMsg, "Great googly moogly! It worked!" ); |
| 183 |
> |
errorCheckPoint(); |
| 184 |
> |
|
| 185 |
> |
#ifdef IS_MPI |
| 186 |
|
MPI_Finalize(); |
| 187 |
|
#endif |
| 188 |
|
|
