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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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. 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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, 234107 (2008). |
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* [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 "brains/SimInfo.hpp" |
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#include "brains/Thermo.hpp" |
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#include "integrators/IntegratorCreator.hpp" |
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#include "integrators/NPA.hpp" |
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#include "primitives/Molecule.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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namespace OpenMD { |
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|
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void NPA::moveA() { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* sd; |
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Vector3d Tb, ji; |
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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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Vector3d sc; |
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int index; |
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|
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loadEta(); |
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|
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instaTemp =thermo.getTemperature(); |
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press = thermo.getPressureTensor(); |
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instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + |
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press(1, 1) + |
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press(2, 2)) / 3.0; |
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instaVol =thermo.getVolume(); |
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|
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Vector3d COM = thermo.getCom(); |
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|
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//evolve velocity half step |
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|
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calcVelScale(); |
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|
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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|
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vel = sd->getVel(); |
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frc = sd->getFrc(); |
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|
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mass = sd->getMass(); |
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|
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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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|
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vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc; |
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sd->setVel(vel); |
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|
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if (sd->isDirectional()) { |
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|
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// get and convert the torque to body frame |
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|
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Tb = sd->lab2Body(sd->getTrq()); |
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|
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// get the angular momentum, and propagate a half step |
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|
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ji = sd->getJ(); |
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|
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ji += dt2*PhysicalConstants::energyConvert * Tb |
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- dt2*thermostat.first* ji; |
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|
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rotAlgo_->rotate(sd, ji, dt); |
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|
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sd->setJ(ji); |
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} |
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} |
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} |
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// evolve eta a half step |
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|
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evolveEtaA(); |
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flucQ_->moveA(); |
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|
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index = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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|
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oldPos[index++] = sd->getPos(); |
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|
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} |
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} |
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|
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//the first estimation of r(t+dt) is equal to r(t) |
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|
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for(int k = 0; k < maxIterNum_; k++) { |
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index = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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|
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vel = sd->getVel(); |
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pos = sd->getPos(); |
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|
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this->getPosScale(pos, COM, index, sc); |
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|
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pos = oldPos[index] + dt * (vel + sc); |
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sd->setPos(pos); |
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|
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++index; |
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} |
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} |
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|
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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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|
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this->scaleSimBox(); |
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|
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saveEta(); |
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} |
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|
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void NPA::moveB(void) { |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* sd; |
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int index; |
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Vector3d Tb; |
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Vector3d ji; |
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Vector3d sc; |
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Vector3d vel; |
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Vector3d frc; |
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RealType mass; |
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|
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loadEta(); |
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|
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//save velocity and angular momentum |
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index = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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|
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oldVel[index] = sd->getVel(); |
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|
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if (sd->isDirectional()) |
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oldJi[index] = sd->getJ(); |
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|
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++index; |
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} |
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} |
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|
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instaVol = thermo.getVolume(); |
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instaTemp = thermo.getTemperature(); |
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instaPress = thermo.getPressure(); |
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|
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//evolve eta |
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this->evolveEtaB(); |
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this->calcVelScale(); |
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|
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index = 0; |
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for (mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i)) { |
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|
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for (sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j)) { |
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|
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frc = sd->getFrc(); |
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mass = sd->getMass(); |
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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 = oldVel[index] |
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+ dt2*PhysicalConstants::energyConvert/mass* frc |
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- dt2*sc; |
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|
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sd->setVel(vel); |
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|
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if (sd->isDirectional()) { |
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// get and convert the torque to body frame |
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Tb = sd->lab2Body(sd->getTrq()); |
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|
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ji = oldJi[index] |
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+ dt2*PhysicalConstants::energyConvert*Tb |
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- dt2*thermostat.first*oldJi[index]; |
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|
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sd->setJ(ji); |
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} |
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|
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++index; |
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} |
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} |
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|
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rattle_->constraintB(); |
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|
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flucQ_->moveB(); |
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saveEta(); |
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} |
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|
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void NPA::evolveEtaA() { |
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|
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eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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oldEta = eta; |
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} |
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|
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void NPA::evolveEtaB() { |
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|
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prevEta = eta; |
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eta(2,2) = oldEta(2, 2) + dt2 * instaVol * |
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(press(2, 2) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2); |
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} |
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|
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void NPA::calcVelScale(){ |
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|
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for (int i = 0; i < 3; i++ ) { |
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for (int j = 0; j < 3; j++ ) { |
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vScale(i, j) = eta(i, j); |
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} |
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} |
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} |
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|
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void NPA::getVelScaleA(Vector3d& sc, const Vector3d& vel){ |
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sc = vScale * vel; |
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} |
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|
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void NPA::getVelScaleB(Vector3d& sc, int index ) { |
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sc = vScale * oldVel[index]; |
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} |
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|
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void NPA::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, |
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Vector3d& sc) { |
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|
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Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM; |
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sc = eta * rj; |
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} |
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|
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void NPA::scaleSimBox(){ |
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Mat3x3d scaleMat; |
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|
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for(int i=0; i<3; i++){ |
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for(int j=0; j<3; j++){ |
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scaleMat(i, j) = 0.0; |
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if(i==j) { |
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scaleMat(i, j) = 1.0; |
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} |
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} |
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} |
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|
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scaleMat(2, 2) = exp(dt*eta(2, 2)); |
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Mat3x3d hmat = snap->getHmat(); |
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hmat = hmat *scaleMat; |
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snap->setHmat(hmat); |
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} |
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|
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bool NPA::etaConverged() { |
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int i; |
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RealType diffEta, sumEta; |
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|
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sumEta = 0; |
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for(i = 0; i < 3; i++) { |
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sumEta += pow(prevEta(i, i) - eta(i, i), 2); |
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} |
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|
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diffEta = sqrt( sumEta / 3.0 ); |
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|
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return ( diffEta <= etaTolerance ); |
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} |
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|
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RealType NPA::calcConservedQuantity(){ |
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|
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thermostat = snap->getThermostat(); |
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loadEta(); |
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|
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of integrableObjects, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
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// than the barostat (when there are particles with orientational degrees |
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// of freedom). |
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fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp; |
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|
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RealType conservedQuantity; |
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RealType totalEnergy; |
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RealType thermostat_kinetic; |
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RealType thermostat_potential; |
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RealType barostat_kinetic; |
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RealType barostat_potential; |
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RealType trEta; |
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|
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totalEnergy = thermo.getTotalEnergy(); |
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|
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thermostat_kinetic = 0.0; |
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thermostat_potential = 0.0; |
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|
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SquareMatrix<RealType, 3> tmp = eta.transpose() * eta; |
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trEta = tmp.trace(); |
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|
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barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert); |
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|
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barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert; |
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|
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conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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return conservedQuantity; |
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|
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} |
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|
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void NPA::loadEta() { |
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eta= snap->getBarostat(); |
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|
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//if (!eta.isDiagonal()) { |
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// sprintf( painCave.errMsg, |
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// "NPA error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix"); |
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// painCave.isFatal = 1; |
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// simError(); |
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//} |
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} |
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|
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void NPA::saveEta() { |
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snap->setBarostat(eta); |
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} |
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|
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} |
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|
