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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 |
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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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
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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 |
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> |
* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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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). |
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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). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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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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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); |
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< |
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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|
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Vector3d sc; |
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Vector3d vel; |
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Vector3d frc; |
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< |
double mass; |
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> |
RealType mass; |
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|
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|
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chi= currentSnapshot_->getChi(); |
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integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
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< |
double oldChi = chi; |
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< |
double prevChi; |
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> |
RealType oldChi = chi; |
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> |
RealType prevChi; |
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|
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loadEta(); |
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|
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getVelScaleB(sc, index); |
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|
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// velocity half step |
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< |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * OOPSEConstant::energyConvert - sc[j]); |
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< |
vel = oldVel[index] + dt2*OOPSEConstant::energyConvert/mass* frc - dt2*sc; |
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> |
//vel[j] = oldVel[3 * i + j] + dt2 *((frc[j] / mass) * PhysicalConstants::energyConvert - sc[j]); |
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> |
vel = oldVel[index] + 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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// get and convert the torque to body frame |
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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|
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< |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi[3*i+j]*chi); |
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< |
ji = oldJi[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi*oldJi[index]; |
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> |
//ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * PhysicalConstants::energyConvert - oldJi[3*i+j]*chi); |
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> |
ji = oldJi[index] + dt2*PhysicalConstants::energyConvert*Tb - dt2*chi*oldJi[index]; |
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integrableObject->setJ(ji); |
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} |
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|
