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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 "math/MatVec3.h" |
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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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|
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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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namespace oopse { |
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Thermo::Thermo(SimInfo *the_info) { info = the_info; } |
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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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Thermo::~Thermo() { } |
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|
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Thermo::~Thermo(){ |
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delete gaussStream; |
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} |
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double Thermo::getKinetic() { |
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const double e_convert = |
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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], |
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aJ[3], |
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I[3][3]; |
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int i, |
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j, |
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k, |
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kl; |
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double Thermo::getKinetic(){ |
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double kinetic_global; |
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vector<StuntDouble *>integrableObjects = info->integrableObjects; |
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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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kinetic = 0.0; |
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kinetic_global = 0.0; |
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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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for( kl = 0; kl < integrableObjects.size(); kl++ ) { |
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aVel = integrableObjects[kl]->getVel(); |
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amass = integrableObjects[kl]->getMass(); |
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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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for( j = 0; j < 3; j++ ) |
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kinetic += amass * aVel[j] * aVel[j]; |
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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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if (integrableObjects[kl]->isDirectional()) { |
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aJ = integrableObjects[kl]->getJ(); |
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integrableObjects[kl]->getI(I); |
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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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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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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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|
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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 / e_convert; |
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|
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return kinetic; |
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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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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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double Thermo::getPotential() { |
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double potential_local; |
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double potential; |
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int el, |
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nSRI; |
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Molecule *molecules; |
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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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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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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} |
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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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// Get total potential for entire system from MPI. |
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|
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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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|
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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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|
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#else |
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potential = potential_local; |
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potential = potential_local; |
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#endif // is_mpi |
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return potential; |
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return potential; |
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} |
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double Thermo::getTotalE(){ |
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double Thermo::getTotalE() { |
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double total; |
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|
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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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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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double Thermo::getTemperature(){ |
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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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const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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temperature |
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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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= ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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double Thermo::getVolume() { |
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return info->boxVol; |
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return temperature; |
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} |
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double Thermo::getVolume() { return info->boxVol; } |
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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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// Relies on the calculation of the full molecular pressure tensor |
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this->getPressureTensor(press); |
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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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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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this->getPressureTensor(press); |
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return pressure; |
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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|
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return pressure; |
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} |
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double Thermo::getPressureX() { |
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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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// Relies on the calculation of the full molecular pressure tensor |
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|
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this->getPressureTensor(press); |
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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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pressureX = p_convert * press[0][0]; |
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this->getPressureTensor(press); |
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return pressureX; |
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pressureX = p_convert * press[0][0]; |
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return pressureX; |
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} |
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double Thermo::getPressureY() { |
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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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// Relies on the calculation of the full molecular pressure tensor |
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|
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this->getPressureTensor(press); |
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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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pressureY = p_convert * press[1][1]; |
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this->getPressureTensor(press); |
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|
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return pressureY; |
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pressureY = p_convert * press[1][1]; |
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|
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return pressureY; |
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} |
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|
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double Thermo::getPressureZ() { |
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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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// Relies on the calculation of the full molecular pressure tensor |
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|
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this->getPressureTensor(press); |
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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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|
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pressureZ = p_convert * press[2][2]; |
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this->getPressureTensor(press); |
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|
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return pressureZ; |
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pressureZ = p_convert * press[2][2]; |
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|
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return pressureZ; |
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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 |
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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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|
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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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const double e_convert = 4.184e - 4; |
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|
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const double e_convert = 4.184e-4; |
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> |
double molmass, |
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volume; |
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double vcom[3]; |
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> |
double p_local[9], |
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p_global[9]; |
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int i, |
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j, |
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> |
k; |
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|
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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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|
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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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|
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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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|
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for (i=0; i < info->integrableObjects.size(); i++) { |
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vcom = info->integrableObjects[i]->getVel(); |
224 |
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|
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p_local[0] += molmass * (vcom[0] * vcom[0]); |
226 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
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> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
228 |
> |
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]); |
231 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
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> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
233 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
234 |
> |
} |
235 |
|
|
236 |
< |
molmass = info->integrableObjects[i]->getMass(); |
217 |
< |
|
218 |
< |
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]); |
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< |
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]); |
236 |
> |
// Get total for entire system from MPI. |
237 |
|
|
230 |
– |
} |
231 |
– |
|
232 |
– |
// Get total for entire system from MPI. |
233 |
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|
238 |
|
#ifdef IS_MPI |
235 |
– |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
236 |
– |
#else |
237 |
– |
for (i=0; i<9; i++) { |
238 |
– |
p_global[i] = p_local[i]; |
239 |
– |
} |
240 |
– |
#endif // is_mpi |
239 |
|
|
240 |
< |
volume = this->getVolume(); |
240 |
> |
MPI_Allreduce(p_local, p_global, 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
241 |
|
|
242 |
+ |
#else |
243 |
|
|
244 |
< |
|
245 |
< |
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; |
244 |
> |
for( i = 0; i < 9; i++ ) { |
245 |
> |
p_global[i] = p_local[i]; |
246 |
|
} |
251 |
– |
} |
252 |
– |
} |
247 |
|
|
248 |
< |
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; |
248 |
> |
#endif // is_mpi |
249 |
|
|
250 |
< |
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 |
< |
} |
250 |
> |
volume = this->getVolume(); |
251 |
|
|
252 |
< |
nobj = info->integrableObjects.size(); |
253 |
< |
|
254 |
< |
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++){ |
284 |
< |
|
285 |
< |
// uses equipartition theory to solve for vbar in angstrom/fs |
252 |
> |
for( i = 0; i < 3; i++ ) { |
253 |
> |
for( j = 0; j < 3; j++ ) { |
254 |
> |
k = 3 * i + j; |
255 |
|
|
256 |
< |
av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
288 |
< |
vbar = sqrt( av2 ); |
256 |
> |
press |
257 |
|
|
258 |
< |
// picks random velocities from a gaussian distribution |
259 |
< |
// centered on vbar |
260 |
< |
|
293 |
< |
for (j=0; j<3; j++) |
294 |
< |
aVel[j] = vbar * gaussStream->getGaussian(); |
295 |
< |
|
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 |
< |
|
258 |
> |
[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
259 |
> |
} |
260 |
> |
} |
261 |
|
} |
262 |
< |
|
346 |
< |
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 |
< |
} |
262 |
> |
} //end namespace oopse |