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#include <cmath> |
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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 "Thermo.hpp" |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#define __C |
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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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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 j, kl; |
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|
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DirectionalAtom *dAtom; |
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|
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int n_atoms; |
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double kinetic_global; |
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Atom** atoms; |
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|
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|
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n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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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 < n_atoms; kl++ ){ |
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|
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atoms[kl]->getVel(aVel); |
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amass = atoms[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( atoms[kl]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[kl]; |
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|
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dAtom->getJ( aJ ); |
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dAtom->getI( I ); |
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|
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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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|
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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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|
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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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|
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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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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} |
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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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|
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#ifdef IS_MPI |
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/* |
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std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
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*/ |
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#endif |
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|
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return potential; |
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} |
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|
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double Thermo::getTotalE(){ |
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|
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double total; |
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|
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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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|
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double Thermo::getTemperature(){ |
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|
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const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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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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|
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double Thermo::getEnthalpy() { |
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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 u, p, v; |
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double press[3][3]; |
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|
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u = this->getTotalE(); |
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|
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this->getPressureTensor(press); |
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p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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|
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v = this->getVolume(); |
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|
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return (u + (p*v)/e_convert); |
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} |
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|
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double Thermo::getVolume() { |
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|
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return info->boxVol; |
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} |
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|
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double Thermo::getPressure() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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const double p_convert = 1.63882576e8; |
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double press[3][3]; |
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double pressure; |
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|
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this->getPressureTensor(press); |
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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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|
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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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|
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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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|
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this->getPressureTensor(press); |
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|
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pressureX = p_convert * press[0][0]; |
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|
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return pressureX; |
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} |
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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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|
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this->getPressureTensor(press); |
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|
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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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|
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this->getPressureTensor(press); |
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|
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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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|
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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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const double e_convert = 4.184e-4; |
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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, nMols; |
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Molecule* molecules; |
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|
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nMols = info->n_mol; |
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molecules = info->molecules; |
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//tau = info->tau; |
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|
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// use velocities of molecular centers of mass and molecular masses: |
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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 < nMols; i++) { |
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molmass = molecules[i].getCOMvel(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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// 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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#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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#endif // is_mpi |
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|
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volume = this->getVolume(); |
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|
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for(i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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k = 3*i + j; |
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press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
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|
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} |
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} |
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} |
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|
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void Thermo::velocitize() { |
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|
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double aVel[3], aJ[3], I[3][3]; |
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int i, j, vr, vd; // velocity randomizer loop counters |
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double vdrift[3]; |
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double vbar; |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
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double av2; |
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double kebar; |
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int n_atoms; |
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Atom** atoms; |
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DirectionalAtom* dAtom; |
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double temperature; |
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int n_oriented; |
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int n_constraints; |
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|
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atoms = info->atoms; |
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n_atoms = info->n_atoms; |
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temperature = info->target_temp; |
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n_oriented = info->n_oriented; |
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n_constraints = info->n_constraints; |
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|
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kebar = kb * temperature * (double)info->ndfRaw / |
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( 2.0 * (double)info->ndf ); |
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|
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for(vr = 0; vr < n_atoms; vr++){ |
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|
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// uses equipartition theory to solve for vbar in angstrom/fs |
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|
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av2 = 2.0 * kebar / atoms[vr]->getMass(); |
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vbar = sqrt( av2 ); |
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|
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// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
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|
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
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|
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for (j=0; j<3; j++) |
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aVel[j] = vbar * gaussStream->getGaussian(); |
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|
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atoms[vr]->setVel( aVel ); |
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|
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} |
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|
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// Get the Center of Mass drift velocity. |
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|
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getCOMVel(vdrift); |
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|
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// Corrects for the center of mass drift. |
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// sums all the momentum and divides by total mass. |
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|
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for(vd = 0; vd < n_atoms; vd++){ |
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|
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atoms[vd]->getVel(aVel); |
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|
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for (j=0; j < 3; j++) |
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aVel[j] -= vdrift[j]; |
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|
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atoms[vd]->setVel( aVel ); |
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} |
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if( n_oriented ){ |
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|
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for( i=0; i<n_atoms; i++ ){ |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getI( I ); |
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|
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for (j = 0 ; j < 3; j++) { |
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|
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vbar = sqrt( 2.0 * kebar * I[j][j] ); |
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aJ[j] = vbar * gaussStream->getGaussian(); |
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|
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} |
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|
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dAtom->setJ( aJ ); |
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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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void Thermo::getCOMVel(double vdrift[3]){ |
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|
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double mtot, mtot_local; |
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double aVel[3], amass; |
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double vdrift_local[3]; |
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int vd, n_atoms, j; |
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Atom** atoms; |
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|
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// We are very careless here with the distinction between n_atoms and n_local |
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// We should really fix this before someone pokes an eye out. |
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|
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n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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|
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mtot_local = 0.0; |
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vdrift_local[0] = 0.0; |
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vdrift_local[1] = 0.0; |
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vdrift_local[2] = 0.0; |
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|
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for(vd = 0; vd < n_atoms; vd++){ |
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|
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amass = atoms[vd]->getMass(); |
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atoms[vd]->getVel( aVel ); |
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|
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for(j = 0; j < 3; j++) |
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vdrift_local[j] += aVel[j] * amass; |
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|
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mtot_local += amass; |
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} |
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|
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#ifdef IS_MPI |
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MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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mtot = mtot_local; |
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for(vd = 0; vd < 3; vd++) { |
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vdrift[vd] = vdrift_local[vd]; |
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} |
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#endif |
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|
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for (vd = 0; vd < 3; vd++) { |
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vdrift[vd] = vdrift[vd] / mtot; |
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} |
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|
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} |
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|
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void Thermo::getCOM(double COM[3]){ |
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|
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double mtot, mtot_local; |
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double aPos[3], amass; |
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double COM_local[3]; |
| 407 |
int i, n_atoms, j; |
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Atom** atoms; |
| 409 |
|
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// We are very careless here with the distinction between n_atoms and n_local |
| 411 |
// We should really fix this before someone pokes an eye out. |
| 412 |
|
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n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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|
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mtot_local = 0.0; |
| 417 |
COM_local[0] = 0.0; |
| 418 |
COM_local[1] = 0.0; |
| 419 |
COM_local[2] = 0.0; |
| 420 |
|
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for(i = 0; i < n_atoms; i++){ |
| 422 |
|
| 423 |
amass = atoms[i]->getMass(); |
| 424 |
atoms[i]->getPos( aPos ); |
| 425 |
|
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for(j = 0; j < 3; j++) |
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COM_local[j] += aPos[j] * amass; |
| 428 |
|
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mtot_local += amass; |
| 430 |
} |
| 431 |
|
| 432 |
#ifdef IS_MPI |
| 433 |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 434 |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 435 |
#else |
| 436 |
mtot = mtot_local; |
| 437 |
for(i = 0; i < 3; i++) { |
| 438 |
COM[i] = COM_local[i]; |
| 439 |
} |
| 440 |
#endif |
| 441 |
|
| 442 |
for (i = 0; i < 3; i++) { |
| 443 |
COM[i] = COM[i] / mtot; |
| 444 |
} |
| 445 |
} |
