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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 <math.h> |
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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/NPT.hpp" |
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#include "math/SquareMatrix3.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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// Basic isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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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 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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|
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Globals* simParams = info_->getSimParams(); |
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|
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if (!simParams->getUseIntialExtendedSystemState()) { |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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currSnapshot->setThermostat(make_pair(0.0, 0.0)); |
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currSnapshot->setBarostat(Mat3x3d(0.0)); |
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} |
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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 = 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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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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|
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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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if (!simParams->haveTargetPressure()) { |
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sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n" |
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" without a targetPressure!\n"); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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targetPressure = simParams->getTargetPressure(); |
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} |
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|
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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 = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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tauBarostat = simParams->getTauBarostat(); |
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} |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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|
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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::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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oldJi.resize(info_->getNIntegrableObjects()); |
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|
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} |
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|
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void NPT::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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thermostat = snap->getThermostat(); |
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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) + 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 = 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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} |
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// evolve chi and eta half step |
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|
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thermostat.first += dt2 * (instaTemp / targetTemp - 1.0) / tt2; |
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|
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evolveEtaA(); |
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|
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//calculate the integral of chidt |
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thermostat.second += dt2 * thermostat.first; |
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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; |
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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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snap->setThermostat(thermostat); |
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|
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saveEta(); |
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} |
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|
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void NPT::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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thermostat = snap->getThermostat(); |
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RealType oldChi = thermostat.first; |
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RealType prevChi; |
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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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// do the iteration: |
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instaVol =thermo.getVolume(); |
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|
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for(int k = 0; k < maxIterNum_; k++) { |
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instaTemp =thermo.getTemperature(); |
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instaPress =thermo.getPressure(); |
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|
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// evolve chi another half step using the temperature at t + dt/2 |
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prevChi = thermostat.first; |
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thermostat.first = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2; |
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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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if ((fabs(prevChi - thermostat.first) <= chiTolerance) && |
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this->etaConverged()) |
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break; |
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} |
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|
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//calculate integral of chidt |
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thermostat.second += dt2 * thermostat.first; |
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|
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snap->setThermostat(thermostat); |
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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 NPT::resetIntegrator(){ |
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snap->setThermostat(make_pair(0.0, 0.0)); |
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resetEta(); |
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} |
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|
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void NPT::resetEta() { |
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Mat3x3d etaMat(0.0); |
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snap->setBarostat(etaMat); |
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} |
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} |
