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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 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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|
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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/OOPSEConstant.hpp" |
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|
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namespace oopse { |
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|
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double 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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double kinetic = 0.0; |
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double 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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double mass = integrableObject->getMass(); |
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Vector3d 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_DOUBLE, 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 / OOPSEConstant::energyConvert; |
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|
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return kinetic; |
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} |
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|
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double Thermo::getPotential() { |
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double potential = 0.0; |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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double 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_DOUBLE, 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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double Thermo::getTotalE() { |
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double 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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double Thermo::getTemperature() { |
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|
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double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb ); |
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return temperature; |
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} |
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|
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double 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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double 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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double pressure; |
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|
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tensor = getPressureTensor(); |
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|
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pressure = OOPSEConstant::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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double 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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double pressure; |
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|
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tensor = getPressureTensor(); |
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|
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pressure = OOPSEConstant::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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|
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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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double 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_DOUBLE, 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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double volume = this->getVolume(); |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d tau = curSnapshot->statData.getTau(); |
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|
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pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
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|
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return pressureTensor; |
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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_X] = tensor(0, 0); |
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stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1); |
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stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2); |
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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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} //end namespace oopse |
