--- trunk/OOPSE/libmdtools/Thermo.cpp 2003/07/15 14:45:09 608 +++ trunk/OOPSE/libmdtools/Thermo.cpp 2004/04/20 16:56:40 1127 @@ -1,4 +1,4 @@ -#include +#include #include using namespace std; \ No newline at end of file @@ -16,12 +16,9 @@ using namespace std; #include "mpiSimulation.hpp" #endif // is_mpi - -#define BASE_SEED 123456789 - -Thermo::Thermo( SimInfo* the_entry_plug ) { - entry_plug = the_entry_plug; - int baseSeed = BASE_SEED; +Thermo::Thermo( SimInfo* the_info ) { + info = the_info; + int baseSeed = the_info->getSeed(); gaussStream = new gaussianSPRNG( baseSeed ); } \ No newline at end of file @@ -36,46 +33,43 @@ double Thermo::getKinetic(){ double kinetic; double amass; double aVel[3], aJ[3], I[3][3]; - int j, kl; + int i, j, k, kl; - DirectionalAtom *dAtom; - - int n_atoms; double kinetic_global; - Atom** atoms; - + vector integrableObjects = info->integrableObjects; - n_atoms = entry_plug->n_atoms; - atoms = entry_plug->atoms; - 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]; - if( atoms[kl]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[kl]; + for (kl=0; klgetVel(aVel); + amass = integrableObjects[kl]->getMass(); - dAtom->getJ( aJ ); - dAtom->getI( I ); - - for (j=0; j<3; j++) - kinetic += aJ[j]*aJ[j] / I[j][j]; - - } + for(j=0; j<3; j++) + kinetic += amass*aVel[j]*aVel[j]; + + if (integrableObjects[kl]->isDirectional()){ + + integrableObjects[kl]->getJ( aJ ); + integrableObjects[kl]->getI( I ); + + if (integrableObjects[kl]->isLinear()) { + i = integrableObjects[kl]->linearAxis(); + j = (i+1)%3; + k = (i+2)%3; + kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k]; + } else { + for (j=0; j<3; j++) + kinetic += aJ[j]*aJ[j] / I[j][j]; + } + } } #ifdef IS_MPI MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); kinetic = kinetic_global; #endif //is_mpi - + kinetic = kinetic * 0.5 / e_convert; return kinetic; \ No newline at end of file @@ -88,14 +82,14 @@ double Thermo::getPotential(){ int el, nSRI; Molecule* molecules; - molecules = entry_plug->molecules; - nSRI = entry_plug->n_SRI; + molecules = info->molecules; + nSRI = info->n_SRI; potential_local = 0.0; potential = 0.0; - potential_local += entry_plug->lrPot; + potential_local += info->lrPot; - for( el=0; eln_mol; el++ ){ + for( el=0; eln_mol; el++ ){ potential_local += molecules[el].getPotential(); } \ No newline at end of file @@ -107,12 +101,6 @@ double Thermo::getPotential(){ potential = potential_local; #endif // is_mpi -#ifdef IS_MPI - /* - std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; - */ -#endif - return potential; } \ No newline at end of file @@ -126,47 +114,76 @@ double Thermo::getTemperature(){ double Thermo::getTemperature(){ - const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) + const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) double temperature; - - temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); + + temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); return temperature; } -double Thermo::getEnthalpy() { +double Thermo::getVolume() { - const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 - double u, p, v; + return info->boxVol; +} + +double Thermo::getPressure() { + + // Relies on the calculation of the full molecular pressure tensor + + const double p_convert = 1.63882576e8; double press[3][3]; + double pressure; - u = this->getTotalE(); + this->getPressureTensor(press); + pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; + + return pressure; +} + +double Thermo::getPressureX() { + + // Relies on the calculation of the full molecular pressure tensor + + const double p_convert = 1.63882576e8; + double press[3][3]; + double pressureX; + this->getPressureTensor(press); - p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; - v = this->getVolume(); + pressureX = p_convert * press[0][0]; - return (u + (p*v)/e_convert); + return pressureX; } -double Thermo::getVolume() { +double Thermo::getPressureY() { - return entry_plug->boxVol; + // Relies on the calculation of the full molecular pressure tensor + + const double p_convert = 1.63882576e8; + double press[3][3]; + double pressureY; + + this->getPressureTensor(press); + + pressureY = p_convert * press[1][1]; + + return pressureY; } -double Thermo::getPressure() { +double Thermo::getPressureZ() { // Relies on the calculation of the full molecular pressure tensor const double p_convert = 1.63882576e8; double press[3][3]; - double pressure; + double pressureZ; this->getPressureTensor(press); - pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; + pressureZ = p_convert * press[2][2]; - return pressure; + return pressureZ; } \ No newline at end of file @@ -180,12 +197,12 @@ void Thermo::getPressureTensor(double press[3][3]){ double molmass, volume; double vcom[3]; double p_local[9], p_global[9]; - int i, j, k, l, nMols; + int i, j, k, nMols; Molecule* molecules; - nMols = entry_plug->n_mol; - molecules = entry_plug->molecules; - //tau = entry_plug->tau; + nMols = info->n_mol; + molecules = info->molecules; + //tau = info->tau; // use velocities of molecular centers of mass and molecular masses: for (i=0; i < 9; i++) { \ No newline at end of file @@ -217,60 +234,78 @@ void Thermo::getPressureTensor(double press[3][3]){ } #endif // is_mpi - volume = entry_plug->boxVol; + volume = this->getVolume(); 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; + press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; + } } } void Thermo::velocitize() { - double x,y; double aVel[3], aJ[3], I[3][3]; - int i, j, vr, vd; // velocity randomizer loop counters + int i, j, l, m, n, 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 n_atoms; - Atom** atoms; - DirectionalAtom* dAtom; double temperature; - int n_oriented; - int n_constraints; + int nobj; - atoms = entry_plug->atoms; - n_atoms = entry_plug->n_atoms; - temperature = entry_plug->target_temp; - n_oriented = entry_plug->n_oriented; - n_constraints = entry_plug->n_constraints; + nobj = info->integrableObjects.size(); - kebar = kb * temperature * (double)entry_plug->ndf / - ( 2.0 * (double)entry_plug->ndfRaw ); + temperature = info->target_temp; - for(vr = 0; vr < n_atoms; vr++){ + kebar = kb * temperature * (double)info->ndfRaw / + ( 2.0 * (double)info->ndf ); + + for(vr = 0; vr < nobj; vr++){ // uses equipartition theory to solve for vbar in angstrom/fs - av2 = 2.0 * kebar / atoms[vr]->getMass(); + av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); vbar = sqrt( av2 ); - -// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); - + // picks random velocities from a gaussian distribution // centered on vbar for (j=0; j<3; j++) aVel[j] = vbar * gaussStream->getGaussian(); - atoms[vr]->setVel( aVel ); + info->integrableObjects[vr]->setVel( aVel ); + + if(info->integrableObjects[vr]->isDirectional()){ + info->integrableObjects[vr]->getI( I ); + + if (info->integrableObjects[vr]->isLinear()) { + + l= info->integrableObjects[vr]->linearAxis(); + m = (l+1)%3; + n = (l+2)%3; + + aJ[l] = 0.0; + vbar = sqrt( 2.0 * kebar * I[m][m] ); + aJ[m] = vbar * gaussStream->getGaussian(); + vbar = sqrt( 2.0 * kebar * I[n][n] ); + aJ[n] = vbar * gaussStream->getGaussian(); + + } else { + for (j = 0 ; j < 3; j++) { + vbar = sqrt( 2.0 * kebar * I[j][j] ); + aJ[j] = vbar * gaussStream->getGaussian(); + } + } // else isLinear + + info->integrableObjects[vr]->setJ( aJ ); + + }//isDirectional + } // Get the Center of Mass drift velocity. \ No newline at end of file @@ -280,36 +315,16 @@ void Thermo::velocitize() { // Corrects for the center of mass drift. // sums all the momentum and divides by total mass. - for(vd = 0; vd < n_atoms; vd++){ + for(vd = 0; vd < nobj; vd++){ - atoms[vd]->getVel(aVel); + info->integrableObjects[vd]->getVel(aVel); for (j=0; j < 3; j++) aVel[j] -= vdrift[j]; - atoms[vd]->setVel( aVel ); + info->integrableObjects[vd]->setVel( aVel ); } - if( n_oriented ){ - - for( i=0; iisDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getI( I ); - - for (j = 0 ; j < 3; j++) { - vbar = sqrt( 2.0 * kebar * I[j][j] ); - aJ[j] = vbar * gaussStream->getGaussian(); - - } - - dAtom->setJ( aJ ); - - } - } - } } void Thermo::getCOMVel(double vdrift[3]){ \ No newline at end of file @@ -317,24 +332,20 @@ void Thermo::getCOMVel(double vdrift[3]){ double mtot, mtot_local; double aVel[3], amass; double vdrift_local[3]; - int vd, n_atoms, j; - Atom** atoms; + int vd, j; + int nobj; - // We are very careless here with the distinction between n_atoms and n_local - // We should really fix this before someone pokes an eye out. + nobj = info->integrableObjects.size(); - n_atoms = entry_plug->n_atoms; - atoms = entry_plug->atoms; - mtot_local = 0.0; vdrift_local[0] = 0.0; vdrift_local[1] = 0.0; vdrift_local[2] = 0.0; - for(vd = 0; vd < n_atoms; vd++){ + for(vd = 0; vd < nobj; vd++){ - amass = atoms[vd]->getMass(); - atoms[vd]->getVel( aVel ); + amass = info->integrableObjects[vd]->getMass(); + info->integrableObjects[vd]->getVel( aVel ); for(j = 0; j < 3; j++) vdrift_local[j] += aVel[j] * amass; \ No newline at end of file @@ -358,3 +369,66 @@ void Thermo::getCOMVel(double vdrift[3]){ } +void Thermo::getCOM(double COM[3]){ + + double mtot, mtot_local; + double aPos[3], amass; + double COM_local[3]; + int i, j; + int nobj; + + mtot_local = 0.0; + COM_local[0] = 0.0; + COM_local[1] = 0.0; + COM_local[2] = 0.0; + + nobj = info->integrableObjects.size(); + for(i = 0; i < nobj; i++){ + + amass = info->integrableObjects[i]->getMass(); + info->integrableObjects[i]->getPos( aPos ); + + for(j = 0; j < 3; j++) + COM_local[j] += aPos[j] * amass; + + mtot_local += amass; + } + +#ifdef IS_MPI + MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); +#else + mtot = mtot_local; + for(i = 0; i < 3; i++) { + COM[i] = COM_local[i]; + } +#endif + + for (i = 0; i < 3; i++) { + COM[i] = COM[i] / mtot; + } +} + +void Thermo::removeCOMdrift() { + double vdrift[3], aVel[3]; + int vd, j, nobj; + + nobj = info->integrableObjects.size(); + + // Get the Center of Mass drift velocity. + + getCOMVel(vdrift); + + // Corrects for the center of mass drift. + // sums all the momentum and divides by total mass. + + for(vd = 0; vd < nobj; vd++){ + + info->integrableObjects[vd]->getVel(aVel); + + for (j=0; j < 3; j++) + aVel[j] -= vdrift[j]; + + info->integrableObjects[vd]->setVel( aVel ); + } +} \ No newline at end of file