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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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#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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#ifdef IS_MPI |
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#define __C |
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//#include "mpiSimulation.hpp" |
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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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#define BASE_SEED 123456789 |
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Thermo::Thermo( SimInfo* the_entry_plug ) { |
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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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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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double potential_local; |
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double potential; |
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int el, nSRI; |
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SRI** sris; |
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Molecule* molecules; |
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|
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sris = entry_plug->sr_interactions; |
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molecules = entry_plug->molecules; |
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nSRI = entry_plug->n_SRI; |
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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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for( el=0; el<nSRI; el++ ){ |
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potential_local += sris[el]->get_potential(); |
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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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// Get total potential for entire system from MPI. |
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
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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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return potential; |
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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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int ndf_local, ndf; |
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ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
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- entry_plug->n_constraints; |
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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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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
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#else |
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ndf = ndf_local; |
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#endif |
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double Thermo::getEnthalpy() { |
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ndf = ndf - 3; |
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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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u = this->getTotalE(); |
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this->getPressureTensor(press); |
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p = (press[0] + press[4] + press[8]) / 3.0; |
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v = this->getVolume(); |
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return (u + (p*v)/e_convert); |
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} |
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double Thermo::getVolume() { |
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double theBox[3]; |
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entry_plug->getBox(theBox); |
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return (theBox[0] * theBox[1] * theBox[2]); |
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} |
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double Thermo::getPressure() { |
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// returns the pressure in units of atm |
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// Relies on the calculation of the full molecular pressure tensor |
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temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
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return temperature; |
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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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this->getPressureTensor(press); |
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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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double Thermo::getPressure(){ |
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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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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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return 0.0; |
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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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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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entry_plug->getBox(theBox); |
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volume = theBox[0] * theBox[1] * theBox[2]; |
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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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void Thermo::velocitize() { |
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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; |
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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 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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n_oriented = entry_plug->n_oriented; |
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n_constraints = entry_plug->n_constraints; |
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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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kebar = kb * temperature * (double)entry_plug->ndf / |
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( 2.0 * (double)entry_plug->ndfRaw ); |
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for(vr = 0; vr < n_atoms; vr++){ |
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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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// picks random velocities from a gaussian distribution |
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// Get the Center of Mass drift velocity. |
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vdrift = getCOMVel(); |
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getCOMVel(vdrift); |
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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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vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
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jy = vbar * gaussStream->getGaussian(); |
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< |
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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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} |
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< |
double* Thermo::getCOMVel(){ |
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> |
void Thermo::getCOMVel(double vdrift[3]){ |
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double mtot, mtot_local; |
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double* vdrift; |
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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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vdrift = new double[3]; |
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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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#ifdef IS_MPI |
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< |
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
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< |
MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM); |
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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[vd] / mtot; |
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} |
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return vdrift; |
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} |
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