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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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|
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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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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 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_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 = entry_plug->molecules; |
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nSRI = entry_plug->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 += entry_plug->lrPot; |
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|
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for( el=0; el<entry_plug->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 = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->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[9]; |
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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] + press[4] + press[8]) / 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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double volume; |
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double Hmat[9]; |
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|
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entry_plug->getBoxM(Hmat); |
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|
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// volume = h1 (dot) h2 (cross) h3 |
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|
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volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
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+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
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+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
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|
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return volume; |
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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[9]; |
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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] + press[4] + press[8]) / 3.0; |
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return pressure; |
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} |
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|
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|
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void Thermo::getPressureTensor(double press[9]){ |
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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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double theBox[3]; |
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//double* tau; |
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int i, nMols; |
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Molecule* molecules; |
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|
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nMols = entry_plug->n_mol; |
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molecules = entry_plug->molecules; |
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//tau = entry_plug->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 = entry_plug->boxVol; |
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|
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for(i=0; i<9; i++) { |
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press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
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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 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 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 = 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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kebar = kb * temperature * (double)entry_plug->ndf / |
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( 2.0 * (double)entry_plug->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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|
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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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|
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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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// 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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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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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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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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|
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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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} |
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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 vdrift_local[3]; |
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int vd, n_atoms; |
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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 = entry_plug->n_atoms; |
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atoms = entry_plug->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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vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
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vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
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vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
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|
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mtot_local += atoms[vd]->getMass(); |
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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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