| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
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|
| 43 |
|
#include "brains/Register.hpp" |
| 50 |
|
#include "integrators/NPTi.hpp" |
| 51 |
|
#include "integrators/NPTf.hpp" |
| 52 |
|
#include "integrators/NPTxyz.hpp" |
| 53 |
+ |
#include "integrators/NPTsz.hpp" |
| 54 |
|
#include "integrators/NPAT.hpp" |
| 55 |
|
#include "integrators/NPrT.hpp" |
| 56 |
+ |
#include "integrators/NgammaT.hpp" |
| 57 |
|
#include "integrators/LangevinDynamics.hpp" |
| 58 |
+ |
#if defined(HAVE_QHULL) |
| 59 |
+ |
#include "integrators/LangevinHullDynamics.hpp" |
| 60 |
+ |
#endif |
| 61 |
|
|
| 62 |
< |
#include "minimizers/MinimizerFactory.hpp" |
| 63 |
< |
#include "minimizers/MinimizerCreator.hpp" |
| 64 |
< |
#include "minimizers/PRCG.hpp" |
| 65 |
< |
#include "minimizers/SDMinimizer.hpp" |
| 66 |
< |
#include "UseTheForce/DUFF.hpp" |
| 67 |
< |
#include "UseTheForce/EAM_FF.hpp" |
| 68 |
< |
#include "UseTheForce/ForceFieldFactory.hpp" |
| 63 |
< |
#include "UseTheForce/ForceFieldCreator.hpp" |
| 64 |
< |
#include "UseTheForce/SHAPES_FF.hpp" |
| 65 |
< |
#include "UseTheForce/SC_FF.hpp" |
| 66 |
< |
#include "UseTheForce/CLAYFF.hpp" |
| 62 |
> |
#include "optimization/OptimizationFactory.hpp" |
| 63 |
> |
#include "optimization/OptimizationCreator.hpp" |
| 64 |
> |
#include "optimization/Method.hpp" |
| 65 |
> |
#include "optimization/SteepestDescent.hpp" |
| 66 |
> |
#include "optimization/ConjugateGradient.hpp" |
| 67 |
> |
#include "optimization/BFGS.hpp" |
| 68 |
> |
|
| 69 |
|
#include "lattice/LatticeFactory.hpp" |
| 70 |
|
#include "lattice/LatticeCreator.hpp" |
| 71 |
|
#include "lattice/FCCLattice.hpp" |
| 72 |
|
|
| 73 |
< |
//#include "openbabel/amberformat.hpp" |
| 74 |
< |
//#include "openbabel/fingerprintformat.hpp" |
| 73 |
< |
//#include "openbabel/gromos96format.hpp" |
| 74 |
< |
#include "openbabel/oopseformat.hpp" |
| 75 |
< |
#include "openbabel/pdbformat.hpp" |
| 76 |
< |
//#include "openbabel/povrayformat.hpp" |
| 77 |
< |
//#include "openbabel/smilesformat.hpp" |
| 78 |
< |
#include "openbabel/tinkerformat.hpp" |
| 79 |
< |
#include "openbabel/xyzformat.hpp" |
| 73 |
> |
using namespace QuantLib; |
| 74 |
> |
namespace OpenMD { |
| 75 |
|
|
| 81 |
– |
|
| 82 |
– |
namespace oopse { |
| 83 |
– |
|
| 84 |
– |
|
| 85 |
– |
void registerForceFields() { |
| 86 |
– |
/** @todo move to a seperate initialization module */ |
| 87 |
– |
//DUFF, WATER and LJ are merged into one force field |
| 88 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("DUFF")); |
| 89 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("WATER")); |
| 90 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<DUFF>("LJ")); |
| 91 |
– |
//in theory, EAM can also be merged |
| 92 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<EAM_FF>("EAM")); |
| 93 |
– |
//heck, that worked... let's try merging SHAPES |
| 94 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SHAPES_FF>("SHAPES")); |
| 95 |
– |
//Well if EAM worked... then Sutton-Chen should work like a CHARMM(Hopefully not). |
| 96 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<SC_FF>("SC")); |
| 97 |
– |
ForceFieldFactory::getInstance()->registerForceField(new ForceFieldBuilder<CLAYFF>("CLAY")); |
| 98 |
– |
} |
| 99 |
– |
|
| 76 |
|
void registerIntegrators() { |
| 77 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVE>("NVE")); |
| 78 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NVT>("NVT")); |
| 82 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPAT>("NPAT")); |
| 83 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPRT")); |
| 84 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NPrT>("NPGT")); |
| 85 |
+ |
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGT")); |
| 86 |
+ |
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<NgammaT>("NGAMMAT")); |
| 87 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LANGEVINDYNAMICS")); |
| 88 |
|
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinDynamics>("LD")); |
| 89 |
< |
|
| 90 |
< |
|
| 89 |
> |
#if defined(HAVE_QHULL) |
| 90 |
> |
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LHULL")); |
| 91 |
> |
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("LANGEVINHULL")); |
| 92 |
> |
IntegratorFactory::getInstance()->registerIntegrator(new IntegratorBuilder<LangevinHullDynamics>("SMIPD")); |
| 93 |
> |
#endif |
| 94 |
|
} |
| 95 |
|
|
| 96 |
< |
void registerMinimizers() { |
| 97 |
< |
MinimizerFactory::getInstance()->registerMinimizer(new MinimizerBuilder<SDMinimizer>("SD")); |
| 98 |
< |
MinimizerFactory::getInstance()->registerMinimizer(new MinimizerBuilder<PRCGMinimizer>("CG")); |
| 96 |
> |
void registerOptimizers() { |
| 97 |
> |
OptimizationFactory::getInstance()->registerOptimization(new OptimizationBuilder<QuantLib::SteepestDescent>("SD")); |
| 98 |
> |
OptimizationFactory::getInstance()->registerOptimization(new OptimizationBuilder<QuantLib::ConjugateGradient>("CG")); |
| 99 |
> |
OptimizationFactory::getInstance()->registerOptimization(new OptimizationBuilder<QuantLib::BFGS>("BFGS")); |
| 100 |
|
} |
| 101 |
|
|
| 102 |
|
void registerLattice(){ |
| 103 |
|
LatticeFactory::getInstance()->registerLattice(new LatticeBuilder<FCCLattice>("FCC")); |
| 104 |
|
} |
| 105 |
|
|
| 124 |
– |
void registerOBFormats(){ |
| 125 |
– |
//static OpenBabel::AmberPrepFormat amberFormatInstance; |
| 126 |
– |
//static OpenBabel::FingerprintFormat fingerprintFormatInstance; |
| 127 |
– |
static OpenBabel::OOPSEFormat oopseFormatInstance; |
| 128 |
– |
static OpenBabel::PDBFormat pdbFormatInstance; |
| 129 |
– |
//static OpenBabel::PovrayFormat povaryFormatInstance; |
| 130 |
– |
//static OpenBabel::SMIFormat smilesFormatInstance; |
| 131 |
– |
static OpenBabel::TinkerFormat tinkerFormatInstance; |
| 132 |
– |
static OpenBabel::XYZFormat xyzFormatInstance; |
| 133 |
– |
} |
| 134 |
– |
|
| 106 |
|
void registerAll() { |
| 136 |
– |
registerForceFields(); |
| 107 |
|
registerIntegrators(); |
| 108 |
< |
registerMinimizers(); |
| 108 |
> |
registerOptimizers(); |
| 109 |
|
} |
| 110 |
|
|
| 111 |
|
} |
