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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
| 10 |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
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* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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* 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 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
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* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "integrators/NVT.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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|
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) { |
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|
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if (!simParams->haveTargetTemp()) { |
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sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
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painCave.isFatal = 1; |
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painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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simError(); |
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} else { |
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targetTemp_ = simParams->getTargetTemp(); |
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} |
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|
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< |
// We must set tauThermostat_. |
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> |
// We must set tauThermostat. |
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|
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if (!simParams->haveTauThermostat()) { |
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sprintf(painCave.errMsg, "If you use the constant temperature\n" |
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"\tintegrator, you must set tauThermostat_.\n"); |
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> |
"\tintegrator, you must set tauThermostat.\n"); |
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|
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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mass = integrableObject->getMass(); |
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|
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// velocity half step (use chi from previous step here): |
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< |
//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi); |
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vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
| 119 |
> |
//vel[j] += dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - vel[j]*chi); |
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> |
vel += dt2 *PhysicalConstants::energyConvert/mass*frc - dt2*chi*vel; |
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|
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// position whole step |
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//pos[j] += dt * vel[j]; |
| 135 |
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|
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ji = integrableObject->getJ(); |
| 137 |
|
|
| 138 |
< |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
| 139 |
< |
ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji; |
| 138 |
> |
//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi); |
| 139 |
> |
ji += dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *ji; |
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rotAlgo->rotate(integrableObject, ji, dt); |
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|
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integrableObject->setJ(ji); |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 184 |
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integrableObject = mol->nextIntegrableObject(j)) { |
| 184 |
– |
oldVel_[index] = integrableObject->getVel(); |
| 185 |
– |
oldJi_[index] = integrableObject->getJ(); |
| 185 |
|
|
| 186 |
+ |
oldVel_[index] = integrableObject->getVel(); |
| 187 |
+ |
|
| 188 |
+ |
if (integrableObject->isDirectional()) |
| 189 |
+ |
oldJi_[index] = integrableObject->getJ(); |
| 190 |
+ |
|
| 191 |
|
++index; |
| 192 |
< |
} |
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< |
|
| 192 |
> |
} |
| 193 |
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} |
| 194 |
|
|
| 195 |
|
// do the iteration: |
| 214 |
|
|
| 215 |
|
// velocity half step |
| 216 |
|
//for(j = 0; j < 3; j++) |
| 217 |
< |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
| 218 |
< |
vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
| 217 |
> |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi); |
| 218 |
> |
vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index]; |
| 219 |
|
|
| 220 |
|
integrableObject->setVel(vel); |
| 221 |
|
|
| 226 |
|
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 227 |
|
|
| 228 |
|
//for(j = 0; j < 3; j++) |
| 229 |
< |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
| 230 |
< |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 229 |
> |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi); |
| 230 |
> |
ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 231 |
|
|
| 232 |
|
integrableObject->setJ(ji); |
| 233 |
|
} |
| 266 |
|
RealType thermostat_kinetic; |
| 267 |
|
RealType thermostat_potential; |
| 268 |
|
|
| 269 |
< |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
| 269 |
> |
fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_; |
| 270 |
|
|
| 271 |
|
Energy = thermo.getTotalE(); |
| 272 |
|
|
| 273 |
< |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 273 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert); |
| 274 |
|
|
| 275 |
< |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 275 |
> |
thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert; |
| 276 |
|
|
| 277 |
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 278 |
|
|
| 280 |
|
} |
| 281 |
|
|
| 282 |
|
|
| 283 |
< |
}//end namespace oopse |
| 283 |
> |
}//end namespace OpenMD |
