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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, 24107 (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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#include <iostream> |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
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|
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#include "brains/Thermo.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "utils/PhysicalConstants.hpp" |
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#include "types/FixedChargeAdapter.hpp" |
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#include "types/FluctuatingChargeAdapter.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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#ifdef HAVE_QHULL |
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#include "math/ConvexHull.hpp" |
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#include "math/AlphaHull.hpp" |
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#endif |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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RealType Thermo::getTranslationalKinetic() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasTranslationalKineticEnergy) { |
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SimInfo::MoleculeIterator miter; |
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vector<StuntDouble*>::iterator iiter; |
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Molecule* mol; |
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StuntDouble* sd; |
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Vector3d vel; |
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RealType mass; |
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RealType kinetic(0.0); |
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|
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for (mol = info_->beginMolecule(miter); mol != NULL; |
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mol = info_->nextMolecule(miter)) { |
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|
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for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
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sd = mol->nextIntegrableObject(iiter)) { |
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|
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mass = sd->getMass(); |
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vel = sd->getVel(); |
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|
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kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
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|
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} |
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} |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE, |
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MPI::SUM); |
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#endif |
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|
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kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
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|
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|
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snap->setTranslationalKineticEnergy(kinetic); |
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} |
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return snap->getTranslationalKineticEnergy(); |
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} |
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|
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RealType Thermo::getRotationalKinetic() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasRotationalKineticEnergy) { |
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SimInfo::MoleculeIterator miter; |
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vector<StuntDouble*>::iterator iiter; |
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Molecule* mol; |
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StuntDouble* sd; |
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Vector3d angMom; |
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Mat3x3d I; |
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int i, j, k; |
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RealType kinetic(0.0); |
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|
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for (mol = info_->beginMolecule(miter); mol != NULL; |
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mol = info_->nextMolecule(miter)) { |
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|
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for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
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sd = mol->nextIntegrableObject(iiter)) { |
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|
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if (sd->isDirectional()) { |
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angMom = sd->getJ(); |
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I = sd->getI(); |
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|
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if (sd->isLinear()) { |
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i = sd->linearAxis(); |
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j = (i + 1) % 3; |
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k = (i + 2) % 3; |
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kinetic += angMom[j] * angMom[j] / I(j, j) |
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+ angMom[k] * angMom[k] / I(k, k); |
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} else { |
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kinetic += angMom[0]*angMom[0]/I(0, 0) |
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+ angMom[1]*angMom[1]/I(1, 1) |
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+ angMom[2]*angMom[2]/I(2, 2); |
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} |
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} |
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} |
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} |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE, |
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MPI::SUM); |
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#endif |
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|
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kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
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|
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snap->setRotationalKineticEnergy(kinetic); |
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} |
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return snap->getRotationalKineticEnergy(); |
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} |
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|
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|
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|
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RealType Thermo::getKinetic() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasKineticEnergy) { |
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RealType ke = getTranslationalKinetic() + getRotationalKinetic(); |
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snap->setKineticEnergy(ke); |
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} |
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return snap->getKineticEnergy(); |
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} |
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|
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RealType Thermo::getPotential() { |
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|
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// ForceManager computes the potential and stores it in the |
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// Snapshot. All we have to do is report it. |
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|
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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return snap->getPotentialEnergy(); |
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} |
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|
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RealType Thermo::getTotalEnergy() { |
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|
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasTotalEnergy) { |
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snap->setTotalEnergy(this->getKinetic() + this->getPotential()); |
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} |
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|
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return snap->getTotalEnergy(); |
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} |
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|
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RealType Thermo::getTemperature() { |
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|
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasTemperature) { |
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|
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RealType temperature = ( 2.0 * this->getKinetic() ) |
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/ (info_->getNdf()* PhysicalConstants::kb ); |
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|
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snap->setTemperature(temperature); |
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} |
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|
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return snap->getTemperature(); |
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} |
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|
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RealType Thermo::getElectronicTemperature() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasElectronicTemperature) { |
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|
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SimInfo::MoleculeIterator miter; |
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vector<Atom*>::iterator iiter; |
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Molecule* mol; |
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Atom* atom; |
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RealType cvel; |
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RealType cmass; |
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RealType kinetic(0.0); |
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RealType eTemp; |
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|
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for (mol = info_->beginMolecule(miter); mol != NULL; |
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mol = info_->nextMolecule(miter)) { |
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|
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for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL; |
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atom = mol->nextFluctuatingCharge(iiter)) { |
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|
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cmass = atom->getChargeMass(); |
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cvel = atom->getFlucQVel(); |
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|
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kinetic += cmass * cvel * cvel; |
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|
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} |
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} |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE, |
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MPI::SUM); |
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#endif |
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|
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kinetic *= 0.5; |
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eTemp = (2.0 * kinetic) / |
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(info_->getNFluctuatingCharges() * PhysicalConstants::kb ); |
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|
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snap->setElectronicTemperature(eTemp); |
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} |
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|
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return snap->getElectronicTemperature(); |
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} |
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|
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|
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RealType Thermo::getVolume() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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return snap->getVolume(); |
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} |
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|
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RealType Thermo::getPressure() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasPressure) { |
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// Relies on the calculation of the full molecular pressure tensor |
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|
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Mat3x3d tensor; |
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RealType pressure; |
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|
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tensor = getPressureTensor(); |
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|
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pressure = PhysicalConstants::pressureConvert * |
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(tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
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|
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snap->setPressure(pressure); |
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} |
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return snap->getPressure(); |
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} |
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|
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Mat3x3d Thermo::getPressureTensor() { |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
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// routine derived via viral theorem description in: |
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// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasPressureTensor) { |
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|
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Mat3x3d pressureTensor; |
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Mat3x3d p_tens(0.0); |
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RealType mass; |
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Vector3d vcom; |
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|
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SimInfo::MoleculeIterator i; |
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vector<StuntDouble*>::iterator j; |
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Molecule* mol; |
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StuntDouble* sd; |
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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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mass = sd->getMass(); |
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vcom = sd->getVel(); |
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p_tens += mass * outProduct(vcom, vcom); |
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} |
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} |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9, |
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MPI::REALTYPE, MPI::SUM); |
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#endif |
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|
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RealType volume = this->getVolume(); |
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Mat3x3d stressTensor = snap->getStressTensor(); |
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|
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pressureTensor = (p_tens + |
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PhysicalConstants::energyConvert * stressTensor)/volume; |
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|
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snap->setPressureTensor(pressureTensor); |
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} |
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return snap->getPressureTensor(); |
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} |
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|
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|
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|
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|
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Vector3d Thermo::getSystemDipole() { |
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Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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if (!snap->hasSystemDipole) { |
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SimInfo::MoleculeIterator miter; |
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vector<Atom*>::iterator aiter; |
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Molecule* mol; |
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Atom* atom; |
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RealType charge; |
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RealType moment(0.0); |
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Vector3d ri(0.0); |
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Vector3d dipoleVector(0.0); |
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Vector3d nPos(0.0); |
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Vector3d pPos(0.0); |
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RealType nChg(0.0); |
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RealType pChg(0.0); |
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int nCount = 0; |
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int pCount = 0; |
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|
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RealType chargeToC = 1.60217733e-19; |
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RealType angstromToM = 1.0e-10; |
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RealType debyeToCm = 3.33564095198e-30; |
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|
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for (mol = info_->beginMolecule(miter); mol != NULL; |
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mol = info_->nextMolecule(miter)) { |
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|
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for (atom = mol->beginAtom(aiter); atom != NULL; |
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atom = mol->nextAtom(aiter)) { |
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|
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charge = 0.0; |
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|
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FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType()); |
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if ( fca.isFixedCharge() ) { |
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charge = fca.getCharge(); |
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} |
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|
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FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType()); |
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if ( fqa.isFluctuatingCharge() ) { |
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charge += atom->getFlucQPos(); |
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} |
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|
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charge *= chargeToC; |
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|
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ri = atom->getPos(); |
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snap->wrapVector(ri); |
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ri *= angstromToM; |
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|
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if (charge < 0.0) { |
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nPos += ri; |
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nChg -= charge; |
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nCount++; |
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} else if (charge > 0.0) { |
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pPos += ri; |
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pChg += charge; |
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pCount++; |
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} |
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|
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if (atom->isDipole()) { |
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dipoleVector += atom->getDipole() * debyeToCm; |
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} |
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} |
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} |
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|
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE, |
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MPI::SUM); |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE, |
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MPI::SUM); |
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|
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER, |
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MPI::SUM); |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER, |
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MPI::SUM); |
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|
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3, |
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MPI::REALTYPE, MPI::SUM); |
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3, |
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MPI::REALTYPE, MPI::SUM); |
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|
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MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(), |
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3, MPI::REALTYPE, MPI::SUM); |
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#endif |
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|
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// first load the accumulated dipole moment (if dipoles were present) |
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Vector3d boxDipole = dipoleVector; |
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// now include the dipole moment due to charges |
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// use the lesser of the positive and negative charge totals |
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RealType chg_value = nChg <= pChg ? nChg : pChg; |
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|
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// find the average positions |
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if (pCount > 0 && nCount > 0 ) { |
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pPos /= pCount; |
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nPos /= nCount; |
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} |
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|
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// dipole is from the negative to the positive (physics notation) |
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boxDipole += (pPos - nPos) * chg_value; |
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snap->setSystemDipole(boxDipole); |
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} |
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|
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return snap->getSystemDipole(); |
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} |
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|
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// Returns the Heat Flux Vector for the system |
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Vector3d Thermo::getHeatFlux(){ |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 425 |
SimInfo::MoleculeIterator miter; |
| 426 |
vector<StuntDouble*>::iterator iiter; |
| 427 |
Molecule* mol; |
| 428 |
StuntDouble* sd; |
| 429 |
RigidBody::AtomIterator ai; |
| 430 |
Atom* atom; |
| 431 |
Vector3d vel; |
| 432 |
Vector3d angMom; |
| 433 |
Mat3x3d I; |
| 434 |
int i; |
| 435 |
int j; |
| 436 |
int k; |
| 437 |
RealType mass; |
| 438 |
|
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Vector3d x_a; |
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RealType kinetic; |
| 441 |
RealType potential; |
| 442 |
RealType eatom; |
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RealType AvgE_a_ = 0; |
| 444 |
// Convective portion of the heat flux |
| 445 |
Vector3d heatFluxJc = V3Zero; |
| 446 |
|
| 447 |
/* Calculate convective portion of the heat flux */ |
| 448 |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 449 |
mol = info_->nextMolecule(miter)) { |
| 450 |
|
| 451 |
for (sd = mol->beginIntegrableObject(iiter); |
| 452 |
sd != NULL; |
| 453 |
sd = mol->nextIntegrableObject(iiter)) { |
| 454 |
|
| 455 |
mass = sd->getMass(); |
| 456 |
vel = sd->getVel(); |
| 457 |
|
| 458 |
kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
| 459 |
|
| 460 |
if (sd->isDirectional()) { |
| 461 |
angMom = sd->getJ(); |
| 462 |
I = sd->getI(); |
| 463 |
|
| 464 |
if (sd->isLinear()) { |
| 465 |
i = sd->linearAxis(); |
| 466 |
j = (i + 1) % 3; |
| 467 |
k = (i + 2) % 3; |
| 468 |
kinetic += angMom[j] * angMom[j] / I(j, j) |
| 469 |
+ angMom[k] * angMom[k] / I(k, k); |
| 470 |
} else { |
| 471 |
kinetic += angMom[0]*angMom[0]/I(0, 0) |
| 472 |
+ angMom[1]*angMom[1]/I(1, 1) |
| 473 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 474 |
} |
| 475 |
} |
| 476 |
|
| 477 |
potential = 0.0; |
| 478 |
|
| 479 |
if (sd->isRigidBody()) { |
| 480 |
RigidBody* rb = dynamic_cast<RigidBody*>(sd); |
| 481 |
for (atom = rb->beginAtom(ai); atom != NULL; |
| 482 |
atom = rb->nextAtom(ai)) { |
| 483 |
potential += atom->getParticlePot(); |
| 484 |
} |
| 485 |
} else { |
| 486 |
potential = sd->getParticlePot(); |
| 487 |
} |
| 488 |
|
| 489 |
potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2 |
| 490 |
// The potential may not be a 1/2 factor |
| 491 |
eatom = (kinetic + potential)/2.0; // amu A^2/fs^2 |
| 492 |
heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3 |
| 493 |
heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3 |
| 494 |
heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3 |
| 495 |
} |
| 496 |
} |
| 497 |
|
| 498 |
/* The J_v vector is reduced in the forceManager so everyone has |
| 499 |
* the global Jv. Jc is computed over the local atoms and must be |
| 500 |
* reduced among all processors. |
| 501 |
*/ |
| 502 |
#ifdef IS_MPI |
| 503 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE, |
| 504 |
MPI::SUM); |
| 505 |
#endif |
| 506 |
|
| 507 |
// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3 |
| 508 |
|
| 509 |
Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() * |
| 510 |
PhysicalConstants::energyConvert; |
| 511 |
|
| 512 |
// Correct for the fact the flux is 1/V (Jc + Jv) |
| 513 |
return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3 |
| 514 |
} |
| 515 |
|
| 516 |
|
| 517 |
Vector3d Thermo::getComVel(){ |
| 518 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 519 |
|
| 520 |
if (!snap->hasCOMvel) { |
| 521 |
|
| 522 |
SimInfo::MoleculeIterator i; |
| 523 |
Molecule* mol; |
| 524 |
|
| 525 |
Vector3d comVel(0.0); |
| 526 |
RealType totalMass(0.0); |
| 527 |
|
| 528 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 529 |
mol = info_->nextMolecule(i)) { |
| 530 |
RealType mass = mol->getMass(); |
| 531 |
totalMass += mass; |
| 532 |
comVel += mass * mol->getComVel(); |
| 533 |
} |
| 534 |
|
| 535 |
#ifdef IS_MPI |
| 536 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE, |
| 537 |
MPI::SUM); |
| 538 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3, |
| 539 |
MPI::REALTYPE, MPI::SUM); |
| 540 |
#endif |
| 541 |
|
| 542 |
comVel /= totalMass; |
| 543 |
snap->setCOMvel(comVel); |
| 544 |
} |
| 545 |
return snap->getCOMvel(); |
| 546 |
} |
| 547 |
|
| 548 |
Vector3d Thermo::getCom(){ |
| 549 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 550 |
|
| 551 |
if (!snap->hasCOM) { |
| 552 |
|
| 553 |
SimInfo::MoleculeIterator i; |
| 554 |
Molecule* mol; |
| 555 |
|
| 556 |
Vector3d com(0.0); |
| 557 |
RealType totalMass(0.0); |
| 558 |
|
| 559 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 560 |
mol = info_->nextMolecule(i)) { |
| 561 |
RealType mass = mol->getMass(); |
| 562 |
totalMass += mass; |
| 563 |
com += mass * mol->getCom(); |
| 564 |
} |
| 565 |
|
| 566 |
#ifdef IS_MPI |
| 567 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE, |
| 568 |
MPI::SUM); |
| 569 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3, |
| 570 |
MPI::REALTYPE, MPI::SUM); |
| 571 |
#endif |
| 572 |
|
| 573 |
com /= totalMass; |
| 574 |
snap->setCOM(com); |
| 575 |
} |
| 576 |
return snap->getCOM(); |
| 577 |
} |
| 578 |
|
| 579 |
/** |
| 580 |
* Returns center of mass and center of mass velocity in one |
| 581 |
* function call. |
| 582 |
*/ |
| 583 |
void Thermo::getComAll(Vector3d &com, Vector3d &comVel){ |
| 584 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 585 |
|
| 586 |
if (!(snap->hasCOM && snap->hasCOMvel)) { |
| 587 |
|
| 588 |
SimInfo::MoleculeIterator i; |
| 589 |
Molecule* mol; |
| 590 |
|
| 591 |
RealType totalMass(0.0); |
| 592 |
|
| 593 |
com = 0.0; |
| 594 |
comVel = 0.0; |
| 595 |
|
| 596 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 597 |
mol = info_->nextMolecule(i)) { |
| 598 |
RealType mass = mol->getMass(); |
| 599 |
totalMass += mass; |
| 600 |
com += mass * mol->getCom(); |
| 601 |
comVel += mass * mol->getComVel(); |
| 602 |
} |
| 603 |
|
| 604 |
#ifdef IS_MPI |
| 605 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE, |
| 606 |
MPI::SUM); |
| 607 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3, |
| 608 |
MPI::REALTYPE, MPI::SUM); |
| 609 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3, |
| 610 |
MPI::REALTYPE, MPI::SUM); |
| 611 |
#endif |
| 612 |
|
| 613 |
com /= totalMass; |
| 614 |
comVel /= totalMass; |
| 615 |
snap->setCOM(com); |
| 616 |
snap->setCOMvel(comVel); |
| 617 |
} |
| 618 |
com = snap->getCOM(); |
| 619 |
comVel = snap->getCOMvel(); |
| 620 |
return; |
| 621 |
} |
| 622 |
|
| 623 |
/** |
| 624 |
* Return intertia tensor for entire system and angular momentum |
| 625 |
* Vector. |
| 626 |
* |
| 627 |
* |
| 628 |
* |
| 629 |
* [ Ixx -Ixy -Ixz ] |
| 630 |
* I =| -Iyx Iyy -Iyz | |
| 631 |
* [ -Izx -Iyz Izz ] |
| 632 |
*/ |
| 633 |
void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor, |
| 634 |
Vector3d &angularMomentum){ |
| 635 |
|
| 636 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 637 |
|
| 638 |
if (!(snap->hasInertiaTensor && snap->hasCOMw)) { |
| 639 |
|
| 640 |
RealType xx = 0.0; |
| 641 |
RealType yy = 0.0; |
| 642 |
RealType zz = 0.0; |
| 643 |
RealType xy = 0.0; |
| 644 |
RealType xz = 0.0; |
| 645 |
RealType yz = 0.0; |
| 646 |
Vector3d com(0.0); |
| 647 |
Vector3d comVel(0.0); |
| 648 |
|
| 649 |
getComAll(com, comVel); |
| 650 |
|
| 651 |
SimInfo::MoleculeIterator i; |
| 652 |
Molecule* mol; |
| 653 |
|
| 654 |
Vector3d thisq(0.0); |
| 655 |
Vector3d thisv(0.0); |
| 656 |
|
| 657 |
RealType thisMass = 0.0; |
| 658 |
|
| 659 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 660 |
mol = info_->nextMolecule(i)) { |
| 661 |
|
| 662 |
thisq = mol->getCom()-com; |
| 663 |
thisv = mol->getComVel()-comVel; |
| 664 |
thisMass = mol->getMass(); |
| 665 |
// Compute moment of intertia coefficients. |
| 666 |
xx += thisq[0]*thisq[0]*thisMass; |
| 667 |
yy += thisq[1]*thisq[1]*thisMass; |
| 668 |
zz += thisq[2]*thisq[2]*thisMass; |
| 669 |
|
| 670 |
// compute products of intertia |
| 671 |
xy += thisq[0]*thisq[1]*thisMass; |
| 672 |
xz += thisq[0]*thisq[2]*thisMass; |
| 673 |
yz += thisq[1]*thisq[2]*thisMass; |
| 674 |
|
| 675 |
angularMomentum += cross( thisq, thisv ) * thisMass; |
| 676 |
} |
| 677 |
|
| 678 |
inertiaTensor(0,0) = yy + zz; |
| 679 |
inertiaTensor(0,1) = -xy; |
| 680 |
inertiaTensor(0,2) = -xz; |
| 681 |
inertiaTensor(1,0) = -xy; |
| 682 |
inertiaTensor(1,1) = xx + zz; |
| 683 |
inertiaTensor(1,2) = -yz; |
| 684 |
inertiaTensor(2,0) = -xz; |
| 685 |
inertiaTensor(2,1) = -yz; |
| 686 |
inertiaTensor(2,2) = xx + yy; |
| 687 |
|
| 688 |
#ifdef IS_MPI |
| 689 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(), |
| 690 |
9, MPI::REALTYPE, MPI::SUM); |
| 691 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, |
| 692 |
angularMomentum.getArrayPointer(), 3, |
| 693 |
MPI::REALTYPE, MPI::SUM); |
| 694 |
#endif |
| 695 |
|
| 696 |
snap->setCOMw(angularMomentum); |
| 697 |
snap->setInertiaTensor(inertiaTensor); |
| 698 |
} |
| 699 |
|
| 700 |
angularMomentum = snap->getCOMw(); |
| 701 |
inertiaTensor = snap->getInertiaTensor(); |
| 702 |
|
| 703 |
return; |
| 704 |
} |
| 705 |
|
| 706 |
// Returns the angular momentum of the system |
| 707 |
Vector3d Thermo::getAngularMomentum(){ |
| 708 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 709 |
|
| 710 |
if (!snap->hasCOMw) { |
| 711 |
|
| 712 |
Vector3d com(0.0); |
| 713 |
Vector3d comVel(0.0); |
| 714 |
Vector3d angularMomentum(0.0); |
| 715 |
|
| 716 |
getComAll(com, comVel); |
| 717 |
|
| 718 |
SimInfo::MoleculeIterator i; |
| 719 |
Molecule* mol; |
| 720 |
|
| 721 |
Vector3d thisr(0.0); |
| 722 |
Vector3d thisp(0.0); |
| 723 |
|
| 724 |
RealType thisMass; |
| 725 |
|
| 726 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 727 |
mol = info_->nextMolecule(i)) { |
| 728 |
thisMass = mol->getMass(); |
| 729 |
thisr = mol->getCom() - com; |
| 730 |
thisp = (mol->getComVel() - comVel) * thisMass; |
| 731 |
|
| 732 |
angularMomentum += cross( thisr, thisp ); |
| 733 |
} |
| 734 |
|
| 735 |
#ifdef IS_MPI |
| 736 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, |
| 737 |
angularMomentum.getArrayPointer(), 3, |
| 738 |
MPI::REALTYPE, MPI::SUM); |
| 739 |
#endif |
| 740 |
|
| 741 |
snap->setCOMw(angularMomentum); |
| 742 |
} |
| 743 |
|
| 744 |
return snap->getCOMw(); |
| 745 |
} |
| 746 |
|
| 747 |
|
| 748 |
/** |
| 749 |
* Returns the Volume of the system based on a ellipsoid with |
| 750 |
* semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
| 751 |
* where R_i are related to the principle inertia moments |
| 752 |
* R_i = sqrt(C*I_i/N), this reduces to |
| 753 |
* V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). |
| 754 |
* See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
| 755 |
*/ |
| 756 |
RealType Thermo::getGyrationalVolume(){ |
| 757 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 758 |
|
| 759 |
if (!snap->hasGyrationalVolume) { |
| 760 |
|
| 761 |
Mat3x3d intTensor; |
| 762 |
RealType det; |
| 763 |
Vector3d dummyAngMom; |
| 764 |
RealType sysconstants; |
| 765 |
RealType geomCnst; |
| 766 |
RealType volume; |
| 767 |
|
| 768 |
geomCnst = 3.0/2.0; |
| 769 |
/* Get the inertial tensor and angular momentum for free*/ |
| 770 |
getInertiaTensor(intTensor, dummyAngMom); |
| 771 |
|
| 772 |
det = intTensor.determinant(); |
| 773 |
sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects()); |
| 774 |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det); |
| 775 |
|
| 776 |
snap->setGyrationalVolume(volume); |
| 777 |
} |
| 778 |
return snap->getGyrationalVolume(); |
| 779 |
} |
| 780 |
|
| 781 |
void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){ |
| 782 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 783 |
|
| 784 |
if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) { |
| 785 |
|
| 786 |
Mat3x3d intTensor; |
| 787 |
Vector3d dummyAngMom; |
| 788 |
RealType sysconstants; |
| 789 |
RealType geomCnst; |
| 790 |
|
| 791 |
geomCnst = 3.0/2.0; |
| 792 |
/* Get the inertia tensor and angular momentum for free*/ |
| 793 |
this->getInertiaTensor(intTensor, dummyAngMom); |
| 794 |
|
| 795 |
detI = intTensor.determinant(); |
| 796 |
sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects()); |
| 797 |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI); |
| 798 |
snap->setGyrationalVolume(volume); |
| 799 |
} else { |
| 800 |
volume = snap->getGyrationalVolume(); |
| 801 |
detI = snap->getInertiaTensor().determinant(); |
| 802 |
} |
| 803 |
return; |
| 804 |
} |
| 805 |
|
| 806 |
RealType Thermo::getTaggedAtomPairDistance(){ |
| 807 |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 808 |
Globals* simParams = info_->getSimParams(); |
| 809 |
|
| 810 |
if (simParams->haveTaggedAtomPair() && |
| 811 |
simParams->havePrintTaggedPairDistance()) { |
| 812 |
if ( simParams->getPrintTaggedPairDistance()) { |
| 813 |
|
| 814 |
pair<int, int> tap = simParams->getTaggedAtomPair(); |
| 815 |
Vector3d pos1, pos2, rab; |
| 816 |
|
| 817 |
#ifdef IS_MPI |
| 818 |
int mol1 = info_->getGlobalMolMembership(tap.first); |
| 819 |
int mol2 = info_->getGlobalMolMembership(tap.second); |
| 820 |
|
| 821 |
int proc1 = info_->getMolToProc(mol1); |
| 822 |
int proc2 = info_->getMolToProc(mol2); |
| 823 |
|
| 824 |
RealType data[3]; |
| 825 |
if (proc1 == worldRank) { |
| 826 |
StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first); |
| 827 |
pos1 = sd1->getPos(); |
| 828 |
data[0] = pos1.x(); |
| 829 |
data[1] = pos1.y(); |
| 830 |
data[2] = pos1.z(); |
| 831 |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 832 |
} else { |
| 833 |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 834 |
pos1 = Vector3d(data); |
| 835 |
} |
| 836 |
|
| 837 |
if (proc2 == worldRank) { |
| 838 |
StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second); |
| 839 |
pos2 = sd2->getPos(); |
| 840 |
data[0] = pos2.x(); |
| 841 |
data[1] = pos2.y(); |
| 842 |
data[2] = pos2.z(); |
| 843 |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 844 |
} else { |
| 845 |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 846 |
pos2 = Vector3d(data); |
| 847 |
} |
| 848 |
#else |
| 849 |
StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first); |
| 850 |
StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second); |
| 851 |
pos1 = at1->getPos(); |
| 852 |
pos2 = at2->getPos(); |
| 853 |
#endif |
| 854 |
rab = pos2 - pos1; |
| 855 |
currSnapshot->wrapVector(rab); |
| 856 |
return rab.length(); |
| 857 |
} |
| 858 |
return 0.0; |
| 859 |
} |
| 860 |
return 0.0; |
| 861 |
} |
| 862 |
|
| 863 |
RealType Thermo::getHullVolume(){ |
| 864 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 865 |
|
| 866 |
#ifdef HAVE_QHULL |
| 867 |
if (!snap->hasHullVolume) { |
| 868 |
Hull* surfaceMesh_; |
| 869 |
|
| 870 |
Globals* simParams = info_->getSimParams(); |
| 871 |
const std::string ht = simParams->getHULL_Method(); |
| 872 |
|
| 873 |
if (ht == "Convex") { |
| 874 |
surfaceMesh_ = new ConvexHull(); |
| 875 |
} else if (ht == "AlphaShape") { |
| 876 |
surfaceMesh_ = new AlphaHull(simParams->getAlpha()); |
| 877 |
} else { |
| 878 |
return 0.0; |
| 879 |
} |
| 880 |
|
| 881 |
// Build a vector of stunt doubles to determine if they are |
| 882 |
// surface atoms |
| 883 |
std::vector<StuntDouble*> localSites_; |
| 884 |
Molecule* mol; |
| 885 |
StuntDouble* sd; |
| 886 |
SimInfo::MoleculeIterator i; |
| 887 |
Molecule::IntegrableObjectIterator j; |
| 888 |
|
| 889 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 890 |
mol = info_->nextMolecule(i)) { |
| 891 |
for (sd = mol->beginIntegrableObject(j); |
| 892 |
sd != NULL; |
| 893 |
sd = mol->nextIntegrableObject(j)) { |
| 894 |
localSites_.push_back(sd); |
| 895 |
} |
| 896 |
} |
| 897 |
|
| 898 |
// Compute surface Mesh |
| 899 |
surfaceMesh_->computeHull(localSites_); |
| 900 |
snap->setHullVolume(surfaceMesh_->getVolume()); |
| 901 |
} |
| 902 |
return snap->getHullVolume(); |
| 903 |
#else |
| 904 |
return 0.0; |
| 905 |
#endif |
| 906 |
} |
| 907 |
} |
