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#include <math.h> |
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#include <iostream> |
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using namespace std; |
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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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#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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#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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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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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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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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double mass = integrableObject->getMass(); |
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Vector3d vel = integrableObject->getVel(); |
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Thermo::~Thermo(){ |
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delete gaussStream; |
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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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double Thermo::getKinetic(){ |
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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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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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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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#ifdef IS_MPI |
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double kinetic_global; |
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vector<StuntDouble *> integrableObjects = info->integrableObjects; |
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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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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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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for(j=0; j<3; j++) |
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kinetic += amass*aVel[j]*aVel[j]; |
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if (integrableObjects[kl]->isDirectional()){ |
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integrableObjects[kl]->getJ( aJ ); |
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integrableObjects[kl]->getI( I ); |
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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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} |
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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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kinetic = kinetic * 0.5 / e_convert; |
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return kinetic; |
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kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert; |
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return kinetic; |
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} |
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double Thermo::getPotential(){ |
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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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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 potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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SimInfo::MoleculeIterator i; |
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Molecule* mol; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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potential_local += mol->getPotential(); |
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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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// Get total potential for entire system from MPI. |
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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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} |
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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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return potential; |
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} |
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MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
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MPI_COMM_WORLD); |
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double Thermo::getTotalE(){ |
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#else |
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double total; |
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potential = potential_local; |
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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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#endif // is_mpi |
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double Thermo::getTemperature(){ |
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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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temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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return temperature; |
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return potential; |
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} |
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double Thermo::getVolume() { |
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double Thermo::getTotalE() { |
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double total; |
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return info->boxVol; |
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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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double Thermo::getPressure() { |
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// Relies on the calculation of the full molecular pressure tensor |
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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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this->getPressureTensor(press); |
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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return pressure; |
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double Thermo::getTemperature() { |
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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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double Thermo::getPressureX() { |
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// Relies on the calculation of the full molecular pressure tensor |
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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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this->getPressureTensor(press); |
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pressureX = p_convert * press[0][0]; |
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return pressureX; |
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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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double Thermo::getPressureY() { |
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double Thermo::getPressure() { |
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// Relies on the calculation of the full molecular pressure tensor |
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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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// Relies on the calculation of the full molecular pressure tensor |
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this->getPressureTensor(press); |
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pressureY = p_convert * press[1][1]; |
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Mat3x3d tensor; |
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double pressure; |
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return pressureY; |
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} |
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tensor = getPressureTensor(); |
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double Thermo::getPressureZ() { |
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pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
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// Relies on the calculation of the full molecular pressure tensor |
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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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this->getPressureTensor(press); |
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pressureZ = p_convert * press[2][2]; |
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return pressureZ; |
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return pressure; |
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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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void Thermo::getPressureTensor(double press[3][3]){ |
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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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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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const double e_convert = 4.184e-4; |
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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; |
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for (i=0; i < 9; i++) { |
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p_local[i] = 0.0; |
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p_global[i] = 0.0; |
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} |
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// use velocities of integrableObjects and their masses: |
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for (i=0; i < info->integrableObjects.size(); i++) { |
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molmass = info->integrableObjects[i]->getMass(); |
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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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info->integrableObjects[i]->getVel(vcom); |
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|
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p_local[0] += molmass * (vcom[0] * vcom[0]); |
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p_local[1] += molmass * (vcom[0] * vcom[1]); |
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p_local[2] += molmass * (vcom[0] * vcom[2]); |
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p_local[3] += molmass * (vcom[1] * vcom[0]); |
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p_local[4] += molmass * (vcom[1] * vcom[1]); |
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p_local[5] += molmass * (vcom[1] * vcom[2]); |
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p_local[6] += molmass * (vcom[2] * vcom[0]); |
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p_local[7] += molmass * (vcom[2] * vcom[1]); |
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p_local[8] += molmass * (vcom[2] * vcom[2]); |
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|
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} |
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|
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// Get total for entire system from MPI. |
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|
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#ifdef IS_MPI |
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MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
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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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< |
for (i=0; i<9; i++) { |
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p_global[i] = p_local[i]; |
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} |
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> |
p_global = p_local; |
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#endif // is_mpi |
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|
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volume = this->getVolume(); |
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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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pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume; |
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|
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|
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< |
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 |
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} |
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> |
return pressureTensor; |
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} |
| 167 |
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|
| 168 |
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void Thermo::velocitize() { |
| 169 |
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|
| 170 |
< |
double aVel[3], aJ[3], I[3][3]; |
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int i, j, l, m, n, vr, vd; // velocity randomizer loop counters |
| 258 |
< |
double vdrift[3]; |
| 259 |
< |
double vbar; |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 261 |
< |
double av2; |
| 262 |
< |
double kebar; |
| 263 |
< |
double temperature; |
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< |
int nobj; |
| 265 |
< |
|
| 266 |
< |
if (!info->have_target_temp) { |
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< |
sprintf( painCave.errMsg, |
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< |
"You can't resample the velocities without a targetTemp!\n" |
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< |
); |
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< |
painCave.isFatal = 1; |
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< |
painCave.severity = OOPSE_ERROR; |
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< |
simError(); |
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< |
return; |
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< |
} |
| 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++){ |
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> |
void Thermo::saveStat(){ |
| 169 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 170 |
> |
Stats& stat = currSnapshot->statData; |
| 171 |
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|
| 172 |
< |
// uses equipartition theory to solve for vbar in angstrom/fs |
| 172 |
> |
stat[Stats::KINETIC_ENERGY] = getKinetic(); |
| 173 |
> |
stat[Stats::POTENTIAL_ENERGY] = getPotential(); |
| 174 |
> |
stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ; |
| 175 |
> |
stat[Stats::TEMPERATURE] = getTemperature(); |
| 176 |
> |
stat[Stats::PRESSURE] = getPressure(); |
| 177 |
> |
stat[Stats::VOLUME] = getVolume(); |
| 178 |
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|
| 179 |
< |
av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
| 180 |
< |
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(); |
| 179 |
> |
/**@todo need refactorying*/ |
| 180 |
> |
//Conserved Quantity is set by integrator and time is set by setTime |
| 181 |
|
|
| 296 |
– |
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 |
– |
|
| 325 |
– |
} |
| 326 |
– |
|
| 327 |
– |
// Get the Center of Mass drift velocity. |
| 328 |
– |
|
| 329 |
– |
getCOMVel(vdrift); |
| 330 |
– |
|
| 331 |
– |
// 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++){ |
| 335 |
– |
|
| 336 |
– |
info->integrableObjects[vd]->getVel(aVel); |
| 337 |
– |
|
| 338 |
– |
for (j=0; j < 3; j++) |
| 339 |
– |
aVel[j] -= vdrift[j]; |
| 340 |
– |
|
| 341 |
– |
info->integrableObjects[vd]->setVel( aVel ); |
| 342 |
– |
} |
| 343 |
– |
|
| 182 |
|
} |
| 183 |
|
|
| 184 |
< |
void Thermo::getCOMVel(double vdrift[3]){ |
| 347 |
< |
|
| 348 |
< |
double mtot, mtot_local; |
| 349 |
< |
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++){ |
| 362 |
< |
|
| 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; |
| 370 |
< |
} |
| 371 |
< |
|
| 372 |
< |
#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 |
< |
} |
| 184 |
> |
} //end namespace oopse |
