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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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using namespace std; |
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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/SRI.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "math/MatVec3.h" |
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#include "utils/OOPSEConstant.hpp" |
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|
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#ifdef IS_MPI |
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#define __C |
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#include "brains/mpiSimulation.hpp" |
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#endif // is_mpi |
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namespace oopse { |
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|
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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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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Thermo::Thermo( SimInfo* the_info ) { |
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info = the_info; |
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int baseSeed = the_info->getSeed(); |
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|
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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|
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Thermo::~Thermo(){ |
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delete gaussStream; |
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} |
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|
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double Thermo::getKinetic(){ |
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|
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
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double kinetic; |
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double amass; |
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double aVel[3], aJ[3], I[3][3]; |
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int i, j, k, kl; |
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|
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double kinetic_global; |
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vector<StuntDouble *> integrableObjects = info->integrableObjects; |
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|
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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|
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for (kl=0; kl<integrableObjects.size(); kl++) { |
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integrableObjects[kl]->getVel(aVel); |
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amass = integrableObjects[kl]->getMass(); |
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|
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for(j=0; j<3; j++) |
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kinetic += amass*aVel[j]*aVel[j]; |
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|
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if (integrableObjects[kl]->isDirectional()){ |
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|
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integrableObjects[kl]->getJ( aJ ); |
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integrableObjects[kl]->getI( I ); |
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|
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if (integrableObjects[kl]->isLinear()) { |
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i = integrableObjects[kl]->linearAxis(); |
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j = (i+1)%3; |
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k = (i+2)%3; |
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kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k]; |
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} else { |
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for (j=0; j<3; j++) |
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kinetic += aJ[j]*aJ[j] / I[j][j]; |
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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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} |
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|
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#ifdef IS_MPI |
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MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
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MPI_SUM, MPI_COMM_WORLD); |
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kinetic = kinetic_global; |
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#endif //is_mpi |
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|
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kinetic = kinetic * 0.5 / e_convert; |
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|
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return kinetic; |
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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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double Thermo::getPotential(){ |
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|
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double potential_local; |
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double potential; |
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int el, nSRI; |
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Molecule* molecules; |
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#endif //is_mpi |
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|
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert; |
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|
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potential_local = 0.0; |
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potential = 0.0; |
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potential_local += info->lrPot; |
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|
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for( el=0; el<info->n_mol; el++ ){ |
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potential_local += molecules[el].getPotential(); |
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return kinetic; |
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} |
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|
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// Get total potential for entire system from MPI. |
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#ifdef IS_MPI |
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MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
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MPI_SUM, MPI_COMM_WORLD); |
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#else |
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potential = potential_local; |
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#endif // is_mpi |
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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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return 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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double Thermo::getTotalE(){ |
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#ifdef IS_MPI |
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|
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double total; |
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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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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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#else |
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|
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double Thermo::getTemperature(){ |
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potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
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|
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const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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#endif // is_mpi |
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|
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temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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return temperature; |
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} |
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return potential; |
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} |
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|
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double Thermo::getVolume() { |
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RealType Thermo::getTotalE() { |
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RealType total; |
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|
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return info->boxVol; |
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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::getPressure() { |
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RealType Thermo::getTemperature() { |
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|
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RealType 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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// Relies on the calculation of the full molecular pressure tensor |
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|
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const double p_convert = 1.63882576e8; |
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double press[3][3]; |
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double pressure; |
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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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this->getPressureTensor(press); |
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RealType Thermo::getPressure() { |
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|
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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// Relies on the calculation of the full molecular pressure tensor |
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|
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return pressure; |
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} |
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|
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< |
double Thermo::getPressureX() { |
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Mat3x3d tensor; |
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> |
RealType pressure; |
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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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const double p_convert = 1.63882576e8; |
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double press[3][3]; |
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double pressureX; |
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> |
tensor = getPressureTensor(); |
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|
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< |
this->getPressureTensor(press); |
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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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< |
pressureX = p_convert * press[0][0]; |
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> |
return pressure; |
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} |
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|
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return pressureX; |
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} |
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> |
RealType Thermo::getPressure(int direction) { |
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|
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< |
double Thermo::getPressureY() { |
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> |
// Relies on the calculation of the full molecular pressure tensor |
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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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< |
const double p_convert = 1.63882576e8; |
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< |
double press[3][3]; |
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< |
double pressureY; |
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> |
|
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> |
Mat3x3d tensor; |
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> |
RealType pressure; |
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|
|
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< |
this->getPressureTensor(press); |
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> |
tensor = getPressureTensor(); |
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|
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< |
pressureY = p_convert * press[1][1]; |
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> |
pressure = OOPSEConstant::pressureConvert * tensor(direction, direction); |
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|
|
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< |
return pressureY; |
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< |
} |
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> |
return pressure; |
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> |
} |
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|
|
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< |
double Thermo::getPressureZ() { |
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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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< |
// Relies on the calculation of the full molecular pressure tensor |
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< |
|
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< |
const double p_convert = 1.63882576e8; |
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< |
double press[3][3]; |
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< |
double pressureZ; |
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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)) { |
| 194 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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> |
integrableObject = mol->nextIntegrableObject(j)) { |
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|
|
| 197 |
< |
this->getPressureTensor(press); |
| 198 |
< |
|
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< |
pressureZ = p_convert * press[2][2]; |
| 200 |
< |
|
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< |
return pressureZ; |
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< |
} |
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< |
|
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< |
|
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< |
void Thermo::getPressureTensor(double press[3][3]){ |
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< |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 197 |
< |
// routine derived via viral theorem description in: |
| 198 |
< |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 199 |
< |
|
| 200 |
< |
const double e_convert = 4.184e-4; |
| 201 |
< |
|
| 202 |
< |
double molmass, volume; |
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< |
double vcom[3]; |
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< |
double p_local[9], p_global[9]; |
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< |
int i, j, k; |
| 206 |
< |
|
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< |
for (i=0; i < 9; i++) { |
| 208 |
< |
p_local[i] = 0.0; |
| 209 |
< |
p_global[i] = 0.0; |
| 210 |
< |
} |
| 211 |
< |
|
| 212 |
< |
// use velocities of integrableObjects and their masses: |
| 213 |
< |
|
| 214 |
< |
for (i=0; i < info->integrableObjects.size(); i++) { |
| 215 |
< |
|
| 216 |
< |
molmass = info->integrableObjects[i]->getMass(); |
| 197 |
> |
RealType mass = integrableObject->getMass(); |
| 198 |
> |
Vector3d vcom = integrableObject->getVel(); |
| 199 |
> |
p_local += mass * outProduct(vcom, vcom); |
| 200 |
> |
} |
| 201 |
> |
} |
| 202 |
|
|
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– |
info->integrableObjects[i]->getVel(vcom); |
| 219 |
– |
|
| 220 |
– |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
| 221 |
– |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
| 222 |
– |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
| 223 |
– |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
| 224 |
– |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 225 |
– |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
| 226 |
– |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
| 227 |
– |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 228 |
– |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
| 229 |
– |
|
| 230 |
– |
} |
| 231 |
– |
|
| 232 |
– |
// Get total for entire system from MPI. |
| 233 |
– |
|
| 203 |
|
#ifdef IS_MPI |
| 204 |
< |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 204 |
> |
MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 205 |
|
#else |
| 206 |
< |
for (i=0; i<9; i++) { |
| 238 |
< |
p_global[i] = p_local[i]; |
| 239 |
< |
} |
| 206 |
> |
p_global = p_local; |
| 207 |
|
#endif // is_mpi |
| 208 |
|
|
| 209 |
< |
volume = this->getVolume(); |
| 210 |
< |
|
| 211 |
< |
|
| 245 |
< |
|
| 246 |
< |
for(i = 0; i < 3; i++) { |
| 247 |
< |
for (j = 0; j < 3; j++) { |
| 248 |
< |
k = 3*i + j; |
| 249 |
< |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
| 250 |
< |
} |
| 251 |
< |
} |
| 252 |
< |
} |
| 253 |
< |
|
| 254 |
< |
void Thermo::velocitize() { |
| 255 |
< |
|
| 256 |
< |
double aVel[3], aJ[3], I[3][3]; |
| 257 |
< |
int i, j, l, m, n, vr, vd; // velocity randomizer loop counters |
| 258 |
< |
double vdrift[3]; |
| 259 |
< |
double vbar; |
| 260 |
< |
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 261 |
< |
double av2; |
| 262 |
< |
double kebar; |
| 263 |
< |
double temperature; |
| 264 |
< |
int nobj; |
| 265 |
< |
|
| 266 |
< |
if (!info->have_target_temp) { |
| 267 |
< |
sprintf( painCave.errMsg, |
| 268 |
< |
"You can't resample the velocities without a targetTemp!\n" |
| 269 |
< |
); |
| 270 |
< |
painCave.isFatal = 1; |
| 271 |
< |
painCave.severity = OOPSE_ERROR; |
| 272 |
< |
simError(); |
| 273 |
< |
return; |
| 274 |
< |
} |
| 275 |
< |
|
| 276 |
< |
nobj = info->integrableObjects.size(); |
| 277 |
< |
|
| 278 |
< |
temperature = info->target_temp; |
| 279 |
< |
|
| 280 |
< |
kebar = kb * temperature * (double)info->ndfRaw / |
| 281 |
< |
( 2.0 * (double)info->ndf ); |
| 282 |
< |
|
| 283 |
< |
for(vr = 0; vr < nobj; vr++){ |
| 209 |
> |
RealType volume = this->getVolume(); |
| 210 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 211 |
> |
Mat3x3d tau = curSnapshot->statData.getTau(); |
| 212 |
|
|
| 213 |
< |
// uses equipartition theory to solve for vbar in angstrom/fs |
| 286 |
< |
|
| 287 |
< |
av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
| 288 |
< |
vbar = sqrt( av2 ); |
| 289 |
< |
|
| 290 |
< |
// picks random velocities from a gaussian distribution |
| 291 |
< |
// centered on vbar |
| 292 |
< |
|
| 293 |
< |
for (j=0; j<3; j++) |
| 294 |
< |
aVel[j] = vbar * gaussStream->getGaussian(); |
| 213 |
> |
pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
| 214 |
|
|
| 215 |
< |
info->integrableObjects[vr]->setVel( aVel ); |
| 297 |
< |
|
| 298 |
< |
if(info->integrableObjects[vr]->isDirectional()){ |
| 299 |
< |
|
| 300 |
< |
info->integrableObjects[vr]->getI( I ); |
| 301 |
< |
|
| 302 |
< |
if (info->integrableObjects[vr]->isLinear()) { |
| 303 |
< |
|
| 304 |
< |
l= info->integrableObjects[vr]->linearAxis(); |
| 305 |
< |
m = (l+1)%3; |
| 306 |
< |
n = (l+2)%3; |
| 307 |
< |
|
| 308 |
< |
aJ[l] = 0.0; |
| 309 |
< |
vbar = sqrt( 2.0 * kebar * I[m][m] ); |
| 310 |
< |
aJ[m] = vbar * gaussStream->getGaussian(); |
| 311 |
< |
vbar = sqrt( 2.0 * kebar * I[n][n] ); |
| 312 |
< |
aJ[n] = vbar * gaussStream->getGaussian(); |
| 313 |
< |
|
| 314 |
< |
} else { |
| 315 |
< |
for (j = 0 ; j < 3; j++) { |
| 316 |
< |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
| 317 |
< |
aJ[j] = vbar * gaussStream->getGaussian(); |
| 318 |
< |
} |
| 319 |
< |
} // else isLinear |
| 320 |
< |
|
| 321 |
< |
info->integrableObjects[vr]->setJ( aJ ); |
| 322 |
< |
|
| 323 |
< |
}//isDirectional |
| 324 |
< |
|
| 215 |
> |
return pressureTensor; |
| 216 |
|
} |
| 217 |
|
|
| 327 |
– |
// Get the Center of Mass drift velocity. |
| 218 |
|
|
| 219 |
< |
getCOMVel(vdrift); |
| 220 |
< |
|
| 221 |
< |
// Corrects for the center of mass drift. |
| 332 |
< |
// sums all the momentum and divides by total mass. |
| 333 |
< |
|
| 334 |
< |
for(vd = 0; vd < nobj; vd++){ |
| 219 |
> |
void Thermo::saveStat(){ |
| 220 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 221 |
> |
Stats& stat = currSnapshot->statData; |
| 222 |
|
|
| 223 |
< |
info->integrableObjects[vd]->getVel(aVel); |
| 224 |
< |
|
| 225 |
< |
for (j=0; j < 3; j++) |
| 226 |
< |
aVel[j] -= vdrift[j]; |
| 227 |
< |
|
| 228 |
< |
info->integrableObjects[vd]->setVel( aVel ); |
| 342 |
< |
} |
| 223 |
> |
stat[Stats::KINETIC_ENERGY] = getKinetic(); |
| 224 |
> |
stat[Stats::POTENTIAL_ENERGY] = getPotential(); |
| 225 |
> |
stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ; |
| 226 |
> |
stat[Stats::TEMPERATURE] = getTemperature(); |
| 227 |
> |
stat[Stats::PRESSURE] = getPressure(); |
| 228 |
> |
stat[Stats::VOLUME] = getVolume(); |
| 229 |
|
|
| 230 |
< |
} |
| 230 |
> |
Mat3x3d tensor =getPressureTensor(); |
| 231 |
> |
stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0); |
| 232 |
> |
stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1); |
| 233 |
> |
stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2); |
| 234 |
|
|
| 346 |
– |
void Thermo::getCOMVel(double vdrift[3]){ |
| 235 |
|
|
| 236 |
< |
double mtot, mtot_local; |
| 237 |
< |
double aVel[3], amass; |
| 350 |
< |
double vdrift_local[3]; |
| 351 |
< |
int vd, j; |
| 352 |
< |
int nobj; |
| 353 |
< |
|
| 354 |
< |
nobj = info->integrableObjects.size(); |
| 355 |
< |
|
| 356 |
< |
mtot_local = 0.0; |
| 357 |
< |
vdrift_local[0] = 0.0; |
| 358 |
< |
vdrift_local[1] = 0.0; |
| 359 |
< |
vdrift_local[2] = 0.0; |
| 360 |
< |
|
| 361 |
< |
for(vd = 0; vd < nobj; vd++){ |
| 236 |
> |
/**@todo need refactorying*/ |
| 237 |
> |
//Conserved Quantity is set by integrator and time is set by setTime |
| 238 |
|
|
| 363 |
– |
amass = info->integrableObjects[vd]->getMass(); |
| 364 |
– |
info->integrableObjects[vd]->getVel( aVel ); |
| 365 |
– |
|
| 366 |
– |
for(j = 0; j < 3; j++) |
| 367 |
– |
vdrift_local[j] += aVel[j] * amass; |
| 368 |
– |
|
| 369 |
– |
mtot_local += amass; |
| 239 |
|
} |
| 240 |
|
|
| 241 |
< |
#ifdef IS_MPI |
| 373 |
< |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 374 |
< |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 375 |
< |
#else |
| 376 |
< |
mtot = mtot_local; |
| 377 |
< |
for(vd = 0; vd < 3; vd++) { |
| 378 |
< |
vdrift[vd] = vdrift_local[vd]; |
| 379 |
< |
} |
| 380 |
< |
#endif |
| 381 |
< |
|
| 382 |
< |
for (vd = 0; vd < 3; vd++) { |
| 383 |
< |
vdrift[vd] = vdrift[vd] / mtot; |
| 384 |
< |
} |
| 385 |
< |
|
| 386 |
< |
} |
| 387 |
< |
|
| 388 |
< |
void Thermo::getCOM(double COM[3]){ |
| 389 |
< |
|
| 390 |
< |
double mtot, mtot_local; |
| 391 |
< |
double aPos[3], amass; |
| 392 |
< |
double COM_local[3]; |
| 393 |
< |
int i, j; |
| 394 |
< |
int nobj; |
| 395 |
< |
|
| 396 |
< |
mtot_local = 0.0; |
| 397 |
< |
COM_local[0] = 0.0; |
| 398 |
< |
COM_local[1] = 0.0; |
| 399 |
< |
COM_local[2] = 0.0; |
| 400 |
< |
|
| 401 |
< |
nobj = info->integrableObjects.size(); |
| 402 |
< |
for(i = 0; i < nobj; i++){ |
| 403 |
< |
|
| 404 |
< |
amass = info->integrableObjects[i]->getMass(); |
| 405 |
< |
info->integrableObjects[i]->getPos( aPos ); |
| 406 |
< |
|
| 407 |
< |
for(j = 0; j < 3; j++) |
| 408 |
< |
COM_local[j] += aPos[j] * amass; |
| 409 |
< |
|
| 410 |
< |
mtot_local += amass; |
| 411 |
< |
} |
| 412 |
< |
|
| 413 |
< |
#ifdef IS_MPI |
| 414 |
< |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 415 |
< |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 416 |
< |
#else |
| 417 |
< |
mtot = mtot_local; |
| 418 |
< |
for(i = 0; i < 3; i++) { |
| 419 |
< |
COM[i] = COM_local[i]; |
| 420 |
< |
} |
| 421 |
< |
#endif |
| 422 |
< |
|
| 423 |
< |
for (i = 0; i < 3; i++) { |
| 424 |
< |
COM[i] = COM[i] / mtot; |
| 425 |
< |
} |
| 426 |
< |
} |
| 427 |
< |
|
| 428 |
< |
void Thermo::removeCOMdrift() { |
| 429 |
< |
double vdrift[3], aVel[3]; |
| 430 |
< |
int vd, j, nobj; |
| 431 |
< |
|
| 432 |
< |
nobj = info->integrableObjects.size(); |
| 433 |
< |
|
| 434 |
< |
// Get the Center of Mass drift velocity. |
| 435 |
< |
|
| 436 |
< |
getCOMVel(vdrift); |
| 437 |
< |
|
| 438 |
< |
// Corrects for the center of mass drift. |
| 439 |
< |
// sums all the momentum and divides by total mass. |
| 440 |
< |
|
| 441 |
< |
for(vd = 0; vd < nobj; vd++){ |
| 442 |
< |
|
| 443 |
< |
info->integrableObjects[vd]->getVel(aVel); |
| 444 |
< |
|
| 445 |
< |
for (j=0; j < 3; j++) |
| 446 |
< |
aVel[j] -= vdrift[j]; |
| 447 |
< |
|
| 448 |
< |
info->integrableObjects[vd]->setVel( aVel ); |
| 449 |
< |
} |
| 450 |
< |
} |
| 241 |
> |
} //end namespace oopse |
