--- trunk/OOPSE/libmdtools/Thermo.cpp 2003/04/03 19:58:24 445 +++ trunk/OOPSE/libmdtools/Thermo.cpp 2003/07/15 14:45:09 608 @@ -4,7 +4,6 @@ using namespace std; #ifdef IS_MPI #include -#include #endif //is_mpi #include "Thermo.hpp" @@ -34,10 +33,10 @@ double Thermo::getKinetic(){ double Thermo::getKinetic(){ const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 - double vx2, vy2, vz2; - double kinetic, v_sqr; - int kl; - double jx2, jy2, jz2; // the square of the angular momentums + double kinetic; + double amass; + double aVel[3], aJ[3], I[3][3]; + int j, kl; DirectionalAtom *dAtom; @@ -52,28 +51,28 @@ double Thermo::getKinetic(){ kinetic = 0.0; kinetic_global = 0.0; for( kl=0; kl < n_atoms; kl++ ){ + + atoms[kl]->getVel(aVel); + amass = atoms[kl]->getMass(); + + for (j=0; j < 3; j++) + kinetic += amass * aVel[j] * aVel[j]; - vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); - vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); - vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); - - v_sqr = vx2 + vy2 + vz2; - kinetic += atoms[kl]->getMass() * v_sqr; - if( atoms[kl]->isDirectional() ){ dAtom = (DirectionalAtom *)atoms[kl]; + + dAtom->getJ( aJ ); + dAtom->getI( I ); - jx2 = dAtom->getJx() * dAtom->getJx(); - jy2 = dAtom->getJy() * dAtom->getJy(); - jz2 = dAtom->getJz() * dAtom->getJz(); + for (j=0; j<3; j++) + kinetic += aJ[j]*aJ[j] / I[j][j]; - kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) - + (jz2 / dAtom->getIzz()); } } #ifdef IS_MPI - MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); + MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, + MPI_SUM, MPI_COMM_WORLD); kinetic = kinetic_global; #endif //is_mpi @@ -100,17 +99,10 @@ double Thermo::getPotential(){ potential_local += molecules[el].getPotential(); } -#ifdef IS_MPI - /* - std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot - << "; pot_local = " << potential_local - << "; pot = " << potential << "\n"; - */ -#endif - // Get total potential for entire system from MPI. #ifdef IS_MPI - MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); + MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, + MPI_SUM, MPI_COMM_WORLD); #else potential = potential_local; #endif // is_mpi @@ -136,44 +128,116 @@ double Thermo::getTemperature(){ const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) double temperature; - int ndf_local, ndf; - ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented - - entry_plug->n_constraints; + temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); + return temperature; +} -#ifdef IS_MPI - MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); -#else - ndf = ndf_local; -#endif +double Thermo::getEnthalpy() { - ndf = ndf - 3; + const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 + double u, p, v; + double press[3][3]; + + u = this->getTotalE(); + + this->getPressureTensor(press); + p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; + + v = this->getVolume(); + + return (u + (p*v)/e_convert); +} + +double Thermo::getVolume() { + + return entry_plug->boxVol; +} + +double Thermo::getPressure() { + + // Relies on the calculation of the full molecular pressure tensor - temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); - return temperature; + const double p_convert = 1.63882576e8; + double press[3][3]; + double pressure; + + this->getPressureTensor(press); + + pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; + + return pressure; } -double Thermo::getPressure(){ - // returns pressure in units amu*fs^-2*Ang^-1 + +void Thermo::getPressureTensor(double press[3][3]){ + // returns pressure tensor in units amu*fs^-2*Ang^-1 // routine derived via viral theorem description in: // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 - return 0.0; + const double e_convert = 4.184e-4; + + double molmass, volume; + double vcom[3]; + double p_local[9], p_global[9]; + int i, j, k, l, nMols; + Molecule* molecules; + + nMols = entry_plug->n_mol; + molecules = entry_plug->molecules; + //tau = entry_plug->tau; + + // use velocities of molecular centers of mass and molecular masses: + for (i=0; i < 9; i++) { + p_local[i] = 0.0; + p_global[i] = 0.0; + } + + for (i=0; i < nMols; i++) { + molmass = molecules[i].getCOMvel(vcom); + + p_local[0] += molmass * (vcom[0] * vcom[0]); + p_local[1] += molmass * (vcom[0] * vcom[1]); + p_local[2] += molmass * (vcom[0] * vcom[2]); + p_local[3] += molmass * (vcom[1] * vcom[0]); + p_local[4] += molmass * (vcom[1] * vcom[1]); + p_local[5] += molmass * (vcom[1] * vcom[2]); + p_local[6] += molmass * (vcom[2] * vcom[0]); + p_local[7] += molmass * (vcom[2] * vcom[1]); + p_local[8] += molmass * (vcom[2] * vcom[2]); + } + + // Get total for entire system from MPI. + +#ifdef IS_MPI + MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); +#else + for (i=0; i<9; i++) { + p_global[i] = p_local[i]; + } +#endif // is_mpi + + volume = entry_plug->boxVol; + + for(i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) { + k = 3*i + j; + l = 3*j + i; + press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume; + } + } } void Thermo::velocitize() { double x,y; - double vx, vy, vz; - double jx, jy, jz; - int i, vr, vd; // velocity randomizer loop counters + double aVel[3], aJ[3], I[3][3]; + int i, j, vr, vd; // velocity randomizer loop counters double vdrift[3]; double vbar; const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. double av2; double kebar; - int ndf, ndf_local; // number of degrees of freedom - int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom int n_atoms; Atom** atoms; DirectionalAtom* dAtom; @@ -187,24 +251,9 @@ void Thermo::velocitize() { n_oriented = entry_plug->n_oriented; n_constraints = entry_plug->n_constraints; - // Raw degrees of freedom that we have to set - ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; - - // Degrees of freedom that can contain kinetic energy - ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented - - entry_plug->n_constraints; + kebar = kb * temperature * (double)entry_plug->ndf / + ( 2.0 * (double)entry_plug->ndfRaw ); -#ifdef IS_MPI - MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); - MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM); -#else - ndfRaw = ndfRaw_local; - ndf = ndf_local; -#endif - ndf = ndf - 3; - - kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); - for(vr = 0; vr < n_atoms; vr++){ // uses equipartition theory to solve for vbar in angstrom/fs @@ -217,13 +266,11 @@ void Thermo::velocitize() { // picks random velocities from a gaussian distribution // centered on vbar - vx = vbar * gaussStream->getGaussian(); - vy = vbar * gaussStream->getGaussian(); - vz = vbar * gaussStream->getGaussian(); + for (j=0; j<3; j++) + aVel[j] = vbar * gaussStream->getGaussian(); + + atoms[vr]->setVel( aVel ); - atoms[vr]->set_vx( vx ); - atoms[vr]->set_vy( vy ); - atoms[vr]->set_vz( vz ); } // Get the Center of Mass drift velocity. @@ -235,17 +282,12 @@ void Thermo::velocitize() { for(vd = 0; vd < n_atoms; vd++){ - vx = atoms[vd]->get_vx(); - vy = atoms[vd]->get_vy(); - vz = atoms[vd]->get_vz(); - - vx -= vdrift[0]; - vy -= vdrift[1]; - vz -= vdrift[2]; + atoms[vd]->getVel(aVel); - atoms[vd]->set_vx(vx); - atoms[vd]->set_vy(vy); - atoms[vd]->set_vz(vz); + for (j=0; j < 3; j++) + aVel[j] -= vdrift[j]; + + atoms[vd]->setVel( aVel ); } if( n_oriented ){ @@ -254,19 +296,17 @@ void Thermo::velocitize() { if( atoms[i]->isDirectional() ){ dAtom = (DirectionalAtom *)atoms[i]; + dAtom->getI( I ); + + for (j = 0 ; j < 3; j++) { - vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); - jx = vbar * gaussStream->getGaussian(); + vbar = sqrt( 2.0 * kebar * I[j][j] ); + aJ[j] = vbar * gaussStream->getGaussian(); - vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); - jy = vbar * gaussStream->getGaussian(); + } - vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); - jz = vbar * gaussStream->getGaussian(); - - dAtom->setJx( jx ); - dAtom->setJy( jy ); - dAtom->setJz( jz ); + dAtom->setJ( aJ ); + } } } @@ -275,8 +315,9 @@ void Thermo::getCOMVel(double vdrift[3]){ void Thermo::getCOMVel(double vdrift[3]){ double mtot, mtot_local; + double aVel[3], amass; double vdrift_local[3]; - int vd, n_atoms; + int vd, n_atoms, j; Atom** atoms; // We are very careless here with the distinction between n_atoms and n_local @@ -292,16 +333,18 @@ void Thermo::getCOMVel(double vdrift[3]){ for(vd = 0; vd < n_atoms; vd++){ - vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); - vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); - vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); + amass = atoms[vd]->getMass(); + atoms[vd]->getVel( aVel ); + + for(j = 0; j < 3; j++) + vdrift_local[j] += aVel[j] * amass; - mtot_local += atoms[vd]->getMass(); + mtot_local += amass; } #ifdef IS_MPI - MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); - MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); + MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); #else mtot = mtot_local; for(vd = 0; vd < 3; vd++) {