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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 |
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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 |
< |
* 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 |
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< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* 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 |
|
* |
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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 |
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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 |
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* research, please cite the appropriate papers when you publish your |
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+ |
* work. Good starting points are: |
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+ |
* |
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+ |
* [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). |
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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 <math.h> |
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#include "integrators/NPT.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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#include "utils/simError.h" |
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|
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// Basic isotropic thermostating and barostating via the Melchionna |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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NPT::NPT(SimInfo* info) : |
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VelocityVerletIntegrator(info), chiTolerance(1e-6), etaTolerance(1e-6), maxIterNum_(4) { |
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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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// We must set tauThermostat |
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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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if (!simParams->haveTauBarostat()) { |
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sprintf(painCave.errMsg, |
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"If you use the NPT integrator, you must set tauBarostat.\n"); |
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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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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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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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NPT::~NPT() { |
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} |
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|
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< |
void NPT::doUpdate() { |
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> |
void NPT::doUpdateSizes() { |
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|
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oldPos.resize(info_->getNIntegrableObjects()); |
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oldVel.resize(info_->getNIntegrableObjects()); |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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Vector3d Tb, ji; |
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< |
double mass; |
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> |
RealType mass; |
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Vector3d vel; |
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Vector3d pos; |
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Vector3d frc; |
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|
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instaTemp =thermo.getTemperature(); |
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press = thermo.getPressureTensor(); |
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< |
instaPress = OOPSEConstant::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; |
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> |
instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; |
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instaVol =thermo.getVolume(); |
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|
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Vector3d COM = info_->getCom(); |
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getVelScaleA(sc, vel); |
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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 - sc[j]); |
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< |
vel += dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
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> |
//vel[j] += dt2 * ((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]); |
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> |
vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc; |
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integrableObject->setVel(vel); |
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|
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if (integrableObject->isDirectional()) { |
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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); |
| 190 |
< |
ji += dt2*OOPSEConstant::energyConvert * Tb - dt2*chi* ji; |
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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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|
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< |
rotAlgo->rotate(integrableObject, ji, dt); |
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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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//calculate the integral of chidt |
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integralOfChidt += dt2 * chi; |
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|
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+ |
flucQ_->moveA(); |
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+ |
|
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+ |
|
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index = 0; |
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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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|
} |
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|
} |
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|
|
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< |
rattle->constraintA(); |
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> |
rattle_->constraintA(); |
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|
} |
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|
|
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|
// Scale the box after all the positions have been moved: |
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|
Vector3d sc; |
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|
Vector3d vel; |
| 262 |
|
Vector3d frc; |
| 263 |
< |
double mass; |
| 263 |
> |
RealType mass; |
| 264 |
|
|
| 265 |
|
|
| 266 |
|
chi= currentSnapshot_->getChi(); |
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|
integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
| 268 |
< |
double oldChi = chi; |
| 269 |
< |
double prevChi; |
| 268 |
> |
RealType oldChi = chi; |
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> |
RealType prevChi; |
| 270 |
|
|
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|
loadEta(); |
| 272 |
|
|
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|
integrableObject = mol->nextIntegrableObject(j)) { |
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|
|
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|
oldVel[index] = integrableObject->getVel(); |
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< |
oldJi[index] = integrableObject->getJ(); |
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> |
|
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> |
if (integrableObject->isDirectional()) |
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> |
oldJi[index] = integrableObject->getJ(); |
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> |
|
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|
++index; |
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|
} |
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|
} |
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|
getVelScaleB(sc, index); |
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|
|
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|
// velocity half step |
| 316 |
< |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]); |
| 317 |
< |
vel = oldVel[index] + dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
| 316 |
> |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]); |
| 317 |
> |
vel = oldVel[index] + dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc; |
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|
integrableObject->setVel(vel); |
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|
|
| 320 |
|
if (integrableObject->isDirectional()) { |
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|
// get and convert the torque to body frame |
| 322 |
|
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 323 |
|
|
| 324 |
< |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi[3*i+j]*chi); |
| 325 |
< |
ji = oldJi[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi*oldJi[index]; |
| 324 |
> |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi[3*i+j]*chi); |
| 325 |
> |
ji = oldJi[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi*oldJi[index]; |
| 326 |
|
integrableObject->setJ(ji); |
| 327 |
|
} |
| 328 |
|
|
| 330 |
|
} |
| 331 |
|
} |
| 332 |
|
|
| 333 |
< |
rattle->constraintB(); |
| 333 |
> |
rattle_->constraintB(); |
| 334 |
|
|
| 335 |
|
if ((fabs(prevChi - chi) <= chiTolerance) && this->etaConverged()) |
| 336 |
|
break; |
| 342 |
|
currentSnapshot_->setChi(chi); |
| 343 |
|
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
| 344 |
|
|
| 345 |
+ |
flucQ_->moveB(); |
| 346 |
|
saveEta(); |
| 347 |
|
} |
| 348 |
|
|
