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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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#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 "LRI.hpp" |
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#include "Integrator.hpp" |
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|
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#define BASE_SEED 123456789 |
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|
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Thermo::Thermo( SimInfo* the_entry_plug ) { |
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entry_plug = the_entry_plug; |
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int baseSeed = BASE_SEED; |
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|
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cerr << "creating thermo stream\n"; |
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gaussStream = new gaussianSPRNG( baseSeed ); |
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cerr << "created thermo stream\n"; |
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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 vx2, vy2, vz2; |
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double kinetic, v_sqr; |
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int kl; |
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double jx2, jy2, jz2; // the square of the angular momentums |
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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 = entry_plug->n_atoms; |
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atoms = entry_plug->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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vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
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vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
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vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
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|
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v_sqr = vx2 + vy2 + vz2; |
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kinetic += atoms[kl]->getMass() * v_sqr; |
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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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jx2 = dAtom->getJx() * dAtom->getJx(); |
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jy2 = dAtom->getJy() * dAtom->getJy(); |
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jz2 = dAtom->getJz() * dAtom->getJz(); |
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|
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kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
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+ (jz2 / dAtom->getIzz()); |
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} |
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} |
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); |
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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; |
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double potential_global; |
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int el, nSRI; |
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SRI** sris; |
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|
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sris = entry_plug->sr_interactions; |
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nSRI = entry_plug->n_SRI; |
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|
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potential = 0.0; |
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potential_global = 0.0; |
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potential += entry_plug->lrPot; |
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|
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// std::cerr << "long range potential: " << potential << "\n"; |
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for( el=0; el<nSRI; el++ ){ |
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|
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potential += sris[el]->get_potential(); |
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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::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM); |
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potential = potential_global; |
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#endif // is_mpi |
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|
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return potential; |
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} |
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|
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double Thermo::getTotalE(){ |
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|
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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 = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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|
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int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
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- entry_plug->n_constraints - 3; |
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|
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temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
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return temperature; |
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} |
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|
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double Thermo::getPressure(){ |
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|
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// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
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// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
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// const double conv_A_m = 1.0E-10; //convert A -> m |
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|
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return 0.0; |
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} |
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|
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void Thermo::velocitize() { |
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|
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double x,y; |
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double vx, vy, vz; |
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double jx, jy, jz; |
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int i, vr, vd; // velocity randomizer loop counters |
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double vdrift[3]; |
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double mtot = 0.0; |
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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 ndf; // number of degrees of freedom |
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int ndfRaw; // the raw number of degrees of freedom |
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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 = entry_plug->atoms; |
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n_atoms = entry_plug->n_atoms; |
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temperature = entry_plug->target_temp; |
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n_oriented = entry_plug->n_oriented; |
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n_constraints = entry_plug->n_constraints; |
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|
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|
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ndfRaw = 3 * n_atoms + 3 * n_oriented; |
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ndf = ndfRaw - n_constraints - 3; |
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kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
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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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#ifndef USE_SPRNG |
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/* If we are using mpi, we need to use the SPRNG random |
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generator. The non drand48 generator will just repeat |
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the same numbers for every node creating a non-gaussian |
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distribution for the simulation. drand48 is fine for the |
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single processor version of the code, but SPRNG should |
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still be preferred for consistency. |
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*/ |
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|
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#ifdef IS_MPI |
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#error "SPRNG random number generator must be used for MPI" |
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#else |
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// warning "Using drand48 for random number generation" |
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#endif // is_mpi |
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|
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x = drand48(); |
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y = drand48(); |
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vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
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|
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x = drand48(); |
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y = drand48(); |
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vy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
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|
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x = drand48(); |
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y = drand48(); |
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vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
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|
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#endif // use_spring |
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|
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#ifdef USE_SPRNG |
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vx = vbar * gaussStream->getGaussian(); |
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vy = vbar * gaussStream->getGaussian(); |
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vz = vbar * gaussStream->getGaussian(); |
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#endif // use_spring |
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|
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atoms[vr]->set_vx( vx ); |
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atoms[vr]->set_vy( vy ); |
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atoms[vr]->set_vz( vz ); |
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} |
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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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mtot = 0.0; |
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vdrift[0] = 0.0; |
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vdrift[1] = 0.0; |
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vdrift[2] = 0.0; |
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for(vd = 0; vd < n_atoms; vd++){ |
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|
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vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
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vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
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vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
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|
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mtot = mtot + atoms[vd]->getMass(); |
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} |
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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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for(vd = 0; vd < n_atoms; vd++){ |
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|
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vx = atoms[vd]->get_vx(); |
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vy = atoms[vd]->get_vy(); |
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vz = atoms[vd]->get_vz(); |
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|
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|
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vx -= vdrift[0]; |
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vy -= vdrift[1]; |
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vz -= vdrift[2]; |
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|
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atoms[vd]->set_vx(vx); |
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atoms[vd]->set_vy(vy); |
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atoms[vd]->set_vz(vz); |
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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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|
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#ifndef USE_SPRNG |
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|
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#ifdef IS_MPI |
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#error "SPRNG random number generator must be used for MPI" |
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#else // is_mpi |
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//warning "Using drand48 for random number generation" |
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#endif // is_MPI |
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|
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vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
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x = drand48(); |
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y = drand48(); |
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jx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
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|
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vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
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x = drand48(); |
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y = drand48(); |
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jy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
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|
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vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
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x = drand48(); |
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y = drand48(); |
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jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y); |
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|
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#else //use_sprng |
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|
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vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
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jx = vbar * gaussStream->getGaussian(); |
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|
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vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
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jy = vbar * gaussStream->getGaussian(); |
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|
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vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
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jz = vbar * gaussStream->getGaussian(); |
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#endif //use_sprng |
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|
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dAtom->setJx( jx ); |
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dAtom->setJy( jy ); |
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dAtom->setJz( jz ); |
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} |
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} |
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} |
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} |
