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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/MultipoleAdapter.hpp" |
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|
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namespace OpenMD { |
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|
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RealType Thermo::getKinetic() { |
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SimInfo::MoleculeIterator miter; |
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std::vector<StuntDouble*>::iterator iiter; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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Vector3d vel; |
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Vector3d angMom; |
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Mat3x3d I; |
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int i; |
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int j; |
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int k; |
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RealType mass; |
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RealType kinetic = 0.0; |
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RealType kinetic_global = 0.0; |
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|
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for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
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for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(iiter)) { |
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|
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mass = integrableObject->getMass(); |
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vel = integrableObject->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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if (integrableObject->isDirectional()) { |
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angMom = integrableObject->getJ(); |
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I = integrableObject->getI(); |
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|
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if (integrableObject->isLinear()) { |
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i = integrableObject->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) + angMom[k] * angMom[k] / I(k, k); |
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} else { |
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kinetic += angMom[0]*angMom[0]/I(0, 0) + 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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|
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#ifdef IS_MPI |
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|
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MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM, |
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MPI_COMM_WORLD); |
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kinetic = kinetic_global; |
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|
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#endif //is_mpi |
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|
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kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
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|
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return kinetic; |
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} |
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|
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RealType Thermo::getPotential() { |
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RealType potential = 0.0; |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
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|
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// Get total potential for entire system from MPI. |
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|
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#ifdef IS_MPI |
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|
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MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM, |
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MPI_COMM_WORLD); |
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potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
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|
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#else |
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|
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potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
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|
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#endif // is_mpi |
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|
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return potential; |
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} |
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|
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RealType Thermo::getTotalE() { |
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RealType total; |
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|
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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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|
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RealType Thermo::getTemperature() { |
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|
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RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb ); |
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return temperature; |
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} |
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|
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RealType Thermo::getElectronicTemperature() { |
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SimInfo::MoleculeIterator miter; |
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std::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 kinetic_global = 0.0; |
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|
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for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
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for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL; |
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atom = mol->nextFluctuatingCharge(iiter)) { |
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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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|
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MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM, |
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MPI_COMM_WORLD); |
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kinetic = kinetic_global; |
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|
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#endif //is_mpi |
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|
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kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert; |
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return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb ); |
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} |
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|
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|
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|
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|
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RealType Thermo::getVolume() { |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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return curSnapshot->getVolume(); |
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} |
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|
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RealType Thermo::getPressure() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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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 * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
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|
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return pressure; |
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} |
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|
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RealType Thermo::getPressure(int direction) { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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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 * tensor(direction, direction); |
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|
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return pressure; |
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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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Mat3x3d pressureTensor; |
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Mat3x3d p_local(0.0); |
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Mat3x3d p_global(0.0); |
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|
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SimInfo::MoleculeIterator i; |
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std::vector<StuntDouble*>::iterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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RealType mass = integrableObject->getMass(); |
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Vector3d vcom = integrableObject->getVel(); |
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p_local += 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_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
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#else |
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p_global = p_local; |
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#endif // is_mpi |
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|
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RealType volume = this->getVolume(); |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d stressTensor = curSnapshot->getStressTensor(); |
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|
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pressureTensor = (p_global + |
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PhysicalConstants::energyConvert * stressTensor)/volume; |
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|
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return pressureTensor; |
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} |
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|
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|
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void Thermo::saveStat(){ |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Stats& stat = currSnapshot->statData; |
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|
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stat[Stats::KINETIC_ENERGY] = getKinetic(); |
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stat[Stats::POTENTIAL_ENERGY] = getPotential(); |
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stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ; |
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stat[Stats::TEMPERATURE] = getTemperature(); |
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stat[Stats::PRESSURE] = getPressure(); |
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stat[Stats::VOLUME] = getVolume(); |
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|
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Mat3x3d tensor =getPressureTensor(); |
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stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0); |
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stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1); |
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stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2); |
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stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0); |
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stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1); |
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stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2); |
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stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0); |
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stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1); |
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stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2); |
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|
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// grab the simulation box dipole moment if specified |
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if (info_->getCalcBoxDipole()){ |
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Vector3d totalDipole = getBoxDipole(); |
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stat[Stats::BOX_DIPOLE_X] = totalDipole(0); |
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stat[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
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stat[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
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} |
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|
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Globals* simParams = info_->getSimParams(); |
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// grab the heat flux if desired |
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if (simParams->havePrintHeatFlux()) { |
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if (simParams->getPrintHeatFlux()){ |
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Vector3d heatFlux = getHeatFlux(); |
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stat[Stats::HEATFLUX_X] = heatFlux(0); |
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stat[Stats::HEATFLUX_Y] = heatFlux(1); |
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stat[Stats::HEATFLUX_Z] = heatFlux(2); |
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} |
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} |
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|
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if (simParams->haveTaggedAtomPair() && |
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simParams->havePrintTaggedPairDistance()) { |
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if ( simParams->getPrintTaggedPairDistance()) { |
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|
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std::pair<int, int> tap = simParams->getTaggedAtomPair(); |
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Vector3d pos1, pos2, rab; |
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|
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#ifdef IS_MPI |
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std::cerr << "tap = " << tap.first << " " << tap.second << std::endl; |
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|
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int mol1 = info_->getGlobalMolMembership(tap.first); |
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int mol2 = info_->getGlobalMolMembership(tap.second); |
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std::cerr << "mols = " << mol1 << " " << mol2 << std::endl; |
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|
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int proc1 = info_->getMolToProc(mol1); |
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int proc2 = info_->getMolToProc(mol2); |
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|
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std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl; |
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|
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RealType data[3]; |
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if (proc1 == worldRank) { |
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StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first); |
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std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl; |
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pos1 = sd1->getPos(); |
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data[0] = pos1.x(); |
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data[1] = pos1.y(); |
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data[2] = pos1.z(); |
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MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
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} else { |
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MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
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pos1 = Vector3d(data); |
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} |
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|
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|
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if (proc2 == worldRank) { |
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StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second); |
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std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl; |
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pos2 = sd2->getPos(); |
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data[0] = pos2.x(); |
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data[1] = pos2.y(); |
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data[2] = pos2.z(); |
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MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
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} else { |
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MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
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pos2 = Vector3d(data); |
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} |
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#else |
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StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first); |
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StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second); |
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pos1 = at1->getPos(); |
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pos2 = at2->getPos(); |
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#endif |
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rab = pos2 - pos1; |
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currSnapshot->wrapVector(rab); |
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stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length(); |
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} |
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} |
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|
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/**@todo need refactorying*/ |
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//Conserved Quantity is set by integrator and time is set by setTime |
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|
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} |
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|
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|
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Vector3d Thermo::getBoxDipole() { |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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SimInfo::MoleculeIterator miter; |
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std::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; |
| 385 |
mol = info_->nextMolecule(miter)) { |
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|
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for (atom = mol->beginAtom(aiter); atom != NULL; |
| 388 |
atom = mol->nextAtom(aiter)) { |
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|
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if (atom->isCharge() ) { |
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charge = 0.0; |
| 392 |
GenericData* data = atom->getAtomType()->getPropertyByName("Charge"); |
| 393 |
if (data != NULL) { |
| 394 |
|
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charge = (dynamic_cast<DoubleGenericData*>(data))->getData(); |
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charge *= chargeToC; |
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|
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ri = atom->getPos(); |
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currSnapshot->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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} |
| 413 |
|
| 414 |
MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType()); |
| 415 |
if (ma.isDipole() ) { |
| 416 |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 417 |
moment = ma.getDipoleMoment(); |
| 418 |
moment *= debyeToCm; |
| 419 |
dipoleVector += u_i * moment; |
| 420 |
} |
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} |
| 422 |
} |
| 423 |
|
| 424 |
|
| 425 |
#ifdef IS_MPI |
| 426 |
RealType pChg_global, nChg_global; |
| 427 |
int pCount_global, nCount_global; |
| 428 |
Vector3d pPos_global, nPos_global, dipVec_global; |
| 429 |
|
| 430 |
MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM, |
| 431 |
MPI_COMM_WORLD); |
| 432 |
pChg = pChg_global; |
| 433 |
MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM, |
| 434 |
MPI_COMM_WORLD); |
| 435 |
nChg = nChg_global; |
| 436 |
MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM, |
| 437 |
MPI_COMM_WORLD); |
| 438 |
pCount = pCount_global; |
| 439 |
MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM, |
| 440 |
MPI_COMM_WORLD); |
| 441 |
nCount = nCount_global; |
| 442 |
MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3, |
| 443 |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 444 |
pPos = pPos_global; |
| 445 |
MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3, |
| 446 |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 447 |
nPos = nPos_global; |
| 448 |
MPI_Allreduce(dipoleVector.getArrayPointer(), |
| 449 |
dipVec_global.getArrayPointer(), 3, |
| 450 |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 451 |
dipoleVector = dipVec_global; |
| 452 |
#endif //is_mpi |
| 453 |
|
| 454 |
// first load the accumulated dipole moment (if dipoles were present) |
| 455 |
Vector3d boxDipole = dipoleVector; |
| 456 |
// now include the dipole moment due to charges |
| 457 |
// use the lesser of the positive and negative charge totals |
| 458 |
RealType chg_value = nChg <= pChg ? nChg : pChg; |
| 459 |
|
| 460 |
// find the average positions |
| 461 |
if (pCount > 0 && nCount > 0 ) { |
| 462 |
pPos /= pCount; |
| 463 |
nPos /= nCount; |
| 464 |
} |
| 465 |
|
| 466 |
// dipole is from the negative to the positive (physics notation) |
| 467 |
boxDipole += (pPos - nPos) * chg_value; |
| 468 |
|
| 469 |
return boxDipole; |
| 470 |
} |
| 471 |
|
| 472 |
// Returns the Heat Flux Vector for the system |
| 473 |
Vector3d Thermo::getHeatFlux(){ |
| 474 |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 475 |
SimInfo::MoleculeIterator miter; |
| 476 |
std::vector<StuntDouble*>::iterator iiter; |
| 477 |
Molecule* mol; |
| 478 |
StuntDouble* integrableObject; |
| 479 |
RigidBody::AtomIterator ai; |
| 480 |
Atom* atom; |
| 481 |
Vector3d vel; |
| 482 |
Vector3d angMom; |
| 483 |
Mat3x3d I; |
| 484 |
int i; |
| 485 |
int j; |
| 486 |
int k; |
| 487 |
RealType mass; |
| 488 |
|
| 489 |
Vector3d x_a; |
| 490 |
RealType kinetic; |
| 491 |
RealType potential; |
| 492 |
RealType eatom; |
| 493 |
RealType AvgE_a_ = 0; |
| 494 |
// Convective portion of the heat flux |
| 495 |
Vector3d heatFluxJc = V3Zero; |
| 496 |
|
| 497 |
/* Calculate convective portion of the heat flux */ |
| 498 |
for (mol = info_->beginMolecule(miter); mol != NULL; |
| 499 |
mol = info_->nextMolecule(miter)) { |
| 500 |
|
| 501 |
for (integrableObject = mol->beginIntegrableObject(iiter); |
| 502 |
integrableObject != NULL; |
| 503 |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 504 |
|
| 505 |
mass = integrableObject->getMass(); |
| 506 |
vel = integrableObject->getVel(); |
| 507 |
|
| 508 |
kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
| 509 |
|
| 510 |
if (integrableObject->isDirectional()) { |
| 511 |
angMom = integrableObject->getJ(); |
| 512 |
I = integrableObject->getI(); |
| 513 |
|
| 514 |
if (integrableObject->isLinear()) { |
| 515 |
i = integrableObject->linearAxis(); |
| 516 |
j = (i + 1) % 3; |
| 517 |
k = (i + 2) % 3; |
| 518 |
kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k); |
| 519 |
} else { |
| 520 |
kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1) |
| 521 |
+ angMom[2]*angMom[2]/I(2, 2); |
| 522 |
} |
| 523 |
} |
| 524 |
|
| 525 |
potential = 0.0; |
| 526 |
|
| 527 |
if (integrableObject->isRigidBody()) { |
| 528 |
RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject); |
| 529 |
for (atom = rb->beginAtom(ai); atom != NULL; |
| 530 |
atom = rb->nextAtom(ai)) { |
| 531 |
potential += atom->getParticlePot(); |
| 532 |
} |
| 533 |
} else { |
| 534 |
potential = integrableObject->getParticlePot(); |
| 535 |
cerr << "ppot = " << potential << "\n"; |
| 536 |
} |
| 537 |
|
| 538 |
potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2 |
| 539 |
// The potential may not be a 1/2 factor |
| 540 |
eatom = (kinetic + potential)/2.0; // amu A^2/fs^2 |
| 541 |
heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3 |
| 542 |
heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3 |
| 543 |
heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3 |
| 544 |
} |
| 545 |
} |
| 546 |
|
| 547 |
std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl; |
| 548 |
|
| 549 |
/* The J_v vector is reduced in fortan so everyone has the global |
| 550 |
* Jv. Jc is computed over the local atoms and must be reduced |
| 551 |
* among all processors. |
| 552 |
*/ |
| 553 |
#ifdef IS_MPI |
| 554 |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE, |
| 555 |
MPI::SUM); |
| 556 |
#endif |
| 557 |
|
| 558 |
// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3 |
| 559 |
|
| 560 |
Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() * |
| 561 |
PhysicalConstants::energyConvert; |
| 562 |
|
| 563 |
std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl; |
| 564 |
std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl; |
| 565 |
|
| 566 |
// Correct for the fact the flux is 1/V (Jc + Jv) |
| 567 |
return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3 |
| 568 |
} |
| 569 |
} //end namespace OpenMD |
