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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: |
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* |
| 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 |
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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 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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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 |
|
* |
| 12 |
< |
* 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. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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). |
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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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tauThermostat_ = simParams->getTauThermostat(); |
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} |
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|
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< |
update(); |
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> |
updateSizes(); |
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} |
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|
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< |
void NVT::doUpdate() { |
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> |
void NVT::doUpdateSizes() { |
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oldVel_.resize(info_->getNIntegrableObjects()); |
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< |
oldJi_.resize(info_->getNIntegrableObjects()); |
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> |
oldJi_.resize(info_->getNIntegrableObjects()); |
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} |
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void NVT::moveA() { |
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SimInfo::MoleculeIterator i; |
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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; |
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> |
//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]; |
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|
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ji = integrableObject->getJ(); |
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|
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< |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
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< |
ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji; |
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< |
rotAlgo->rotate(integrableObject, ji, dt); |
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> |
//ji[j] += dt2 * (Tb[j] * PhysicalConstants::energyConvert - ji[j]*chi); |
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> |
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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} |
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|
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} |
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|
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< |
rattle->constraintA(); |
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> |
flucQ_->moveA(); |
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> |
rattle_->constraintA(); |
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|
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// Finally, evolve chi a half step (just like a velocity) using |
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// temperature at time t, not time t+dt/2 |
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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; |
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|
integrableObject = mol->nextIntegrableObject(j)) { |
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– |
oldVel_[index] = integrableObject->getVel(); |
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– |
oldJi_[index] = integrableObject->getJ(); |
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|
|
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+ |
oldVel_[index] = integrableObject->getVel(); |
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+ |
|
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+ |
if (integrableObject->isDirectional()) |
| 190 |
+ |
oldJi_[index] = integrableObject->getJ(); |
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+ |
|
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|
++index; |
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< |
} |
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< |
|
| 193 |
> |
} |
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} |
| 195 |
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|
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// do the iteration: |
| 215 |
|
|
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// velocity half step |
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//for(j = 0; j < 3; j++) |
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< |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
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< |
vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
| 218 |
> |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * PhysicalConstants::energyConvert - oldVel_[3*i + j]*chi); |
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> |
vel = oldVel_[index] + dt2/mass*PhysicalConstants::energyConvert * frc - dt2*chi*oldVel_[index]; |
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|
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|
integrableObject->setVel(vel); |
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|
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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|
|
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|
//for(j = 0; j < 3; j++) |
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< |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
| 231 |
< |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 230 |
> |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi_[3*i+j]*chi); |
| 231 |
> |
ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 232 |
|
|
| 233 |
|
integrableObject->setJ(ji); |
| 234 |
|
} |
| 238 |
|
} |
| 239 |
|
} |
| 240 |
|
|
| 241 |
+ |
rattle_->constraintB(); |
| 242 |
|
|
| 238 |
– |
rattle->constraintB(); |
| 239 |
– |
|
| 243 |
|
if (fabs(prevChi - chi) <= chiTolerance_) |
| 244 |
|
break; |
| 245 |
|
|
| 246 |
|
} |
| 247 |
|
|
| 248 |
< |
integralOfChidt += dt2 * chi; |
| 248 |
> |
flucQ_->moveB(); |
| 249 |
|
|
| 250 |
+ |
integralOfChidt += dt2 * chi; |
| 251 |
|
currentSnapshot_->setChi(chi); |
| 252 |
|
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 253 |
|
} |
| 267 |
|
RealType thermostat_kinetic; |
| 268 |
|
RealType thermostat_potential; |
| 269 |
|
|
| 270 |
< |
fkBT = info_->getNdf() *OOPSEConstant::kB *targetTemp_; |
| 270 |
> |
fkBT = info_->getNdf() *PhysicalConstants::kB *targetTemp_; |
| 271 |
|
|
| 272 |
|
Energy = thermo.getTotalE(); |
| 273 |
|
|
| 274 |
< |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 274 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * PhysicalConstants::energyConvert); |
| 275 |
|
|
| 276 |
< |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 276 |
> |
thermostat_potential = fkBT * integralOfChidt / PhysicalConstants::energyConvert; |
| 277 |
|
|
| 278 |
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 279 |
|
|
| 281 |
|
} |
| 282 |
|
|
| 283 |
|
|
| 284 |
< |
}//end namespace oopse |
| 284 |
> |
}//end namespace OpenMD |
