| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "integrators/NVT.hpp" |
| 44 |
|
#include "primitives/Molecule.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
< |
#include "utils/OOPSEConstant.hpp" |
| 46 |
> |
#include "utils/PhysicalConstants.hpp" |
| 47 |
|
|
| 48 |
< |
namespace oopse { |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
|
| 50 |
< |
NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), chiTolerance_ (1e-6), maxIterNum_(4) { |
| 50 |
> |
NVT::NVT(SimInfo* info) : VelocityVerletIntegrator(info), maxIterNum_(4), |
| 51 |
> |
chiTolerance_(1e-6) { |
| 52 |
|
|
| 53 |
|
Globals* simParams = info_->getSimParams(); |
| 54 |
|
|
| 55 |
|
if (!simParams->getUseIntialExtendedSystemState()) { |
| 56 |
< |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 57 |
< |
currSnapshot->setChi(0.0); |
| 56 |
< |
currSnapshot->setIntegralOfChiDt(0.0); |
| 56 |
> |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 57 |
> |
snap->setThermostat(make_pair(0.0, 0.0)); |
| 58 |
|
} |
| 59 |
|
|
| 60 |
|
if (!simParams->haveTargetTemp()) { |
| 61 |
|
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
| 62 |
|
painCave.isFatal = 1; |
| 63 |
< |
painCave.severity = OOPSE_ERROR; |
| 63 |
> |
painCave.severity = OPENMD_ERROR; |
| 64 |
|
simError(); |
| 65 |
|
} else { |
| 66 |
|
targetTemp_ = simParams->getTargetTemp(); |
| 67 |
|
} |
| 68 |
|
|
| 69 |
< |
// We must set tauThermostat_. |
| 69 |
> |
// We must set tauThermostat. |
| 70 |
|
|
| 71 |
|
if (!simParams->haveTauThermostat()) { |
| 72 |
|
sprintf(painCave.errMsg, "If you use the constant temperature\n" |
| 73 |
< |
"\tintegrator, you must set tauThermostat_.\n"); |
| 73 |
> |
"\tintegrator, you must set tauThermostat.\n"); |
| 74 |
|
|
| 75 |
< |
painCave.severity = OOPSE_ERROR; |
| 75 |
> |
painCave.severity = OPENMD_ERROR; |
| 76 |
|
painCave.isFatal = 1; |
| 77 |
|
simError(); |
| 78 |
|
} else { |
| 79 |
|
tauThermostat_ = simParams->getTauThermostat(); |
| 80 |
|
} |
| 81 |
|
|
| 82 |
< |
update(); |
| 82 |
> |
updateSizes(); |
| 83 |
|
} |
| 84 |
|
|
| 85 |
< |
void NVT::doUpdate() { |
| 85 |
> |
void NVT::doUpdateSizes() { |
| 86 |
|
oldVel_.resize(info_->getNIntegrableObjects()); |
| 87 |
< |
oldJi_.resize(info_->getNIntegrableObjects()); |
| 87 |
> |
oldJi_.resize(info_->getNIntegrableObjects()); |
| 88 |
|
} |
| 89 |
+ |
|
| 90 |
|
void NVT::moveA() { |
| 91 |
|
SimInfo::MoleculeIterator i; |
| 92 |
|
Molecule::IntegrableObjectIterator j; |
| 93 |
|
Molecule* mol; |
| 94 |
< |
StuntDouble* integrableObject; |
| 94 |
> |
StuntDouble* sd; |
| 95 |
|
Vector3d Tb; |
| 96 |
|
Vector3d ji; |
| 97 |
< |
double mass; |
| 97 |
> |
RealType mass; |
| 98 |
|
Vector3d vel; |
| 99 |
|
Vector3d pos; |
| 100 |
|
Vector3d frc; |
| 101 |
|
|
| 102 |
< |
double chi = currentSnapshot_->getChi(); |
| 103 |
< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 102 |
< |
|
| 102 |
> |
pair<RealType, RealType> thermostat = snap->getThermostat(); |
| 103 |
> |
|
| 104 |
|
// We need the temperature at time = t for the chi update below: |
| 105 |
|
|
| 106 |
< |
double instTemp = thermo.getTemperature(); |
| 106 |
> |
RealType instTemp = thermo.getTemperature(); |
| 107 |
|
|
| 108 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 109 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 109 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 108 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 109 |
> |
mol = info_->nextMolecule(i)) { |
| 110 |
|
|
| 111 |
< |
vel = integrableObject->getVel(); |
| 112 |
< |
pos = integrableObject->getPos(); |
| 113 |
< |
frc = integrableObject->getFrc(); |
| 111 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 112 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 113 |
|
|
| 114 |
< |
mass = integrableObject->getMass(); |
| 114 |
> |
vel = sd->getVel(); |
| 115 |
> |
pos = sd->getPos(); |
| 116 |
> |
frc = sd->getFrc(); |
| 117 |
|
|
| 118 |
< |
// velocity half step (use chi from previous step here): |
| 119 |
< |
//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi); |
| 120 |
< |
vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
| 118 |
> |
mass = sd->getMass(); |
| 119 |
> |
|
| 120 |
> |
// velocity half step (use chi from previous step here): |
| 121 |
> |
vel += dt2 *PhysicalConstants::energyConvert/mass*frc |
| 122 |
> |
- dt2*thermostat.first*vel; |
| 123 |
|
|
| 124 |
|
// position whole step |
| 122 |
– |
//pos[j] += dt * vel[j]; |
| 125 |
|
pos += dt * vel; |
| 126 |
|
|
| 127 |
< |
integrableObject->setVel(vel); |
| 128 |
< |
integrableObject->setPos(pos); |
| 127 |
> |
sd->setVel(vel); |
| 128 |
> |
sd->setPos(pos); |
| 129 |
|
|
| 130 |
< |
if (integrableObject->isDirectional()) { |
| 130 |
> |
if (sd->isDirectional()) { |
| 131 |
|
|
| 132 |
|
//convert the torque to body frame |
| 133 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 133 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 134 |
|
|
| 135 |
|
// get the angular momentum, and propagate a half step |
| 136 |
|
|
| 137 |
< |
ji = integrableObject->getJ(); |
| 137 |
> |
ji = sd->getJ(); |
| 138 |
|
|
| 139 |
< |
//ji[j] += dt2 * (Tb[j] * OOPSEConstant::energyConvert - ji[j]*chi); |
| 140 |
< |
ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *ji; |
| 139 |
< |
rotAlgo->rotate(integrableObject, ji, dt); |
| 139 |
> |
ji += dt2*PhysicalConstants::energyConvert*Tb |
| 140 |
> |
- dt2*thermostat.first *ji; |
| 141 |
|
|
| 142 |
< |
integrableObject->setJ(ji); |
| 142 |
> |
rotAlgo_->rotate(sd, ji, dt); |
| 143 |
> |
|
| 144 |
> |
sd->setJ(ji); |
| 145 |
|
} |
| 146 |
|
} |
| 147 |
|
|
| 148 |
|
} |
| 149 |
|
|
| 150 |
< |
rattle->constraintA(); |
| 150 |
> |
flucQ_->moveA(); |
| 151 |
> |
rattle_->constraintA(); |
| 152 |
|
|
| 153 |
|
// Finally, evolve chi a half step (just like a velocity) using |
| 154 |
|
// temperature at time t, not time t+dt/2 |
| 155 |
|
|
| 156 |
< |
|
| 157 |
< |
chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 158 |
< |
integralOfChidt += chi * dt2; |
| 156 |
> |
thermostat.first += dt2 * (instTemp / targetTemp_ - 1.0) |
| 157 |
> |
/ (tauThermostat_ * tauThermostat_); |
| 158 |
> |
thermostat.second += thermostat.first * dt2; |
| 159 |
|
|
| 160 |
< |
currentSnapshot_->setChi(chi); |
| 157 |
< |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 160 |
> |
snap->setThermostat(thermostat); |
| 161 |
|
} |
| 162 |
|
|
| 163 |
|
void NVT::moveB() { |
| 164 |
|
SimInfo::MoleculeIterator i; |
| 165 |
|
Molecule::IntegrableObjectIterator j; |
| 166 |
|
Molecule* mol; |
| 167 |
< |
StuntDouble* integrableObject; |
| 167 |
> |
StuntDouble* sd; |
| 168 |
|
|
| 169 |
|
Vector3d Tb; |
| 170 |
|
Vector3d ji; |
| 171 |
|
Vector3d vel; |
| 172 |
|
Vector3d frc; |
| 173 |
< |
double mass; |
| 174 |
< |
double instTemp; |
| 173 |
> |
RealType mass; |
| 174 |
> |
RealType instTemp; |
| 175 |
|
int index; |
| 176 |
|
// Set things up for the iteration: |
| 177 |
|
|
| 178 |
< |
double chi = currentSnapshot_->getChi(); |
| 179 |
< |
double oldChi = chi; |
| 180 |
< |
double prevChi; |
| 178 |
< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 178 |
> |
pair<RealType, RealType> thermostat = snap->getThermostat(); |
| 179 |
> |
RealType oldChi = thermostat.first; |
| 180 |
> |
RealType prevChi; |
| 181 |
|
|
| 182 |
|
index = 0; |
| 183 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 184 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 183 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 184 |
< |
oldVel_[index] = integrableObject->getVel(); |
| 185 |
< |
oldJi_[index] = integrableObject->getJ(); |
| 183 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 184 |
> |
mol = info_->nextMolecule(i)) { |
| 185 |
|
|
| 186 |
+ |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 187 |
+ |
sd = mol->nextIntegrableObject(j)) { |
| 188 |
+ |
|
| 189 |
+ |
oldVel_[index] = sd->getVel(); |
| 190 |
+ |
|
| 191 |
+ |
if (sd->isDirectional()) |
| 192 |
+ |
oldJi_[index] = sd->getJ(); |
| 193 |
+ |
|
| 194 |
|
++index; |
| 195 |
< |
} |
| 189 |
< |
|
| 195 |
> |
} |
| 196 |
|
} |
| 197 |
|
|
| 198 |
|
// do the iteration: |
| 203 |
|
|
| 204 |
|
// evolve chi another half step using the temperature at t + dt/2 |
| 205 |
|
|
| 206 |
< |
prevChi = chi; |
| 207 |
< |
chi = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 206 |
> |
prevChi = thermostat.first; |
| 207 |
> |
thermostat.first = oldChi + dt2 * (instTemp / targetTemp_ - 1.0) |
| 208 |
> |
/ (tauThermostat_ * tauThermostat_); |
| 209 |
|
|
| 210 |
< |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 211 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 212 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 210 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 211 |
> |
mol = info_->nextMolecule(i)) { |
| 212 |
> |
|
| 213 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 214 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 215 |
|
|
| 216 |
< |
frc = integrableObject->getFrc(); |
| 217 |
< |
vel = integrableObject->getVel(); |
| 216 |
> |
frc = sd->getFrc(); |
| 217 |
> |
mass = sd->getMass(); |
| 218 |
|
|
| 210 |
– |
mass = integrableObject->getMass(); |
| 211 |
– |
|
| 219 |
|
// velocity half step |
| 220 |
< |
//for(j = 0; j < 3; j++) |
| 221 |
< |
// vel[j] = oldVel_[3*i+j] + dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - oldVel_[3*i + j]*chi); |
| 222 |
< |
vel = oldVel_[index] + dt2/mass*OOPSEConstant::energyConvert * frc - dt2*chi*oldVel_[index]; |
| 220 |
> |
|
| 221 |
> |
vel = oldVel_[index] |
| 222 |
> |
+ dt2/mass*PhysicalConstants::energyConvert * frc |
| 223 |
> |
- dt2*thermostat.first*oldVel_[index]; |
| 224 |
|
|
| 225 |
< |
integrableObject->setVel(vel); |
| 225 |
> |
sd->setVel(vel); |
| 226 |
|
|
| 227 |
< |
if (integrableObject->isDirectional()) { |
| 227 |
> |
if (sd->isDirectional()) { |
| 228 |
|
|
| 229 |
|
// get and convert the torque to body frame |
| 230 |
|
|
| 231 |
< |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 231 |
> |
Tb = sd->lab2Body(sd->getTrq()); |
| 232 |
|
|
| 233 |
< |
//for(j = 0; j < 3; j++) |
| 234 |
< |
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
| 227 |
< |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
| 233 |
> |
ji = oldJi_[index] + dt2*PhysicalConstants::energyConvert*Tb |
| 234 |
> |
- dt2*thermostat.first *oldJi_[index]; |
| 235 |
|
|
| 236 |
< |
integrableObject->setJ(ji); |
| 236 |
> |
sd->setJ(ji); |
| 237 |
|
} |
| 238 |
|
|
| 239 |
|
|
| 241 |
|
} |
| 242 |
|
} |
| 243 |
|
|
| 244 |
+ |
rattle_->constraintB(); |
| 245 |
|
|
| 246 |
< |
rattle->constraintB(); |
| 239 |
< |
|
| 240 |
< |
if (fabs(prevChi - chi) <= chiTolerance_) |
| 246 |
> |
if (fabs(prevChi - thermostat.first) <= chiTolerance_) |
| 247 |
|
break; |
| 248 |
|
|
| 249 |
|
} |
| 250 |
|
|
| 251 |
< |
integralOfChidt += dt2 * chi; |
| 251 |
> |
flucQ_->moveB(); |
| 252 |
|
|
| 253 |
< |
currentSnapshot_->setChi(chi); |
| 254 |
< |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 253 |
> |
thermostat.second += dt2 * thermostat.first; |
| 254 |
> |
snap->setThermostat(thermostat); |
| 255 |
|
} |
| 256 |
|
|
| 257 |
|
void NVT::resetIntegrator() { |
| 258 |
< |
currentSnapshot_->setChi(0.0); |
| 253 |
< |
currentSnapshot_->setIntegralOfChiDt(0.0); |
| 258 |
> |
snap->setThermostat(make_pair(0.0, 0.0)); |
| 259 |
|
} |
| 260 |
|
|
| 261 |
< |
double NVT::calcConservedQuantity() { |
| 261 |
> |
RealType NVT::calcConservedQuantity() { |
| 262 |
|
|
| 263 |
< |
double chi = currentSnapshot_->getChi(); |
| 264 |
< |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 265 |
< |
double conservedQuantity; |
| 266 |
< |
double fkBT; |
| 267 |
< |
double Energy; |
| 268 |
< |
double thermostat_kinetic; |
| 264 |
< |
double thermostat_potential; |
| 263 |
> |
pair<RealType, RealType> thermostat = snap->getThermostat(); |
| 264 |
> |
RealType conservedQuantity; |
| 265 |
> |
RealType fkBT; |
| 266 |
> |
RealType Energy; |
| 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(); |
| 272 |
> |
Energy = thermo.getTotalEnergy(); |
| 273 |
|
|
| 274 |
< |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * OOPSEConstant::energyConvert); |
| 274 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * thermostat.first * thermostat.first / (2.0 * PhysicalConstants::energyConvert); |
| 275 |
|
|
| 276 |
< |
thermostat_potential = fkBT * integralOfChidt / OOPSEConstant::energyConvert; |
| 276 |
> |
thermostat_potential = fkBT * thermostat.second / PhysicalConstants::energyConvert; |
| 277 |
|
|
| 278 |
|
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 279 |
|
|
| 281 |
|
} |
| 282 |
|
|
| 283 |
|
|
| 284 |
< |
}//end namespace oopse |
| 284 |
> |
}//end namespace OpenMD |
