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#include <cmath> |
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#include <math.h> |
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#include <iostream> |
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using namespace std; |
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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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entry_plug = the_entry_plug; |
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int baseSeed = BASE_SEED; |
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Thermo::Thermo( SimInfo* the_info ) { |
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info = the_info; |
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int baseSeed = the_info->getSeed(); |
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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double Thermo::getKinetic(){ |
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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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double kinetic; |
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double amass; |
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double aVel[3], aJ[3], I[3][3]; |
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int i, j, k, kl; |
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DirectionalAtom *dAtom; |
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int n_atoms; |
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double kinetic_global; |
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Atom** atoms; |
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vector<StuntDouble *> integrableObjects = info->integrableObjects; |
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n_atoms = entry_plug->n_atoms; |
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atoms = entry_plug->atoms; |
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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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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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for (kl=0; kl<integrableObjects.size(); kl++) { |
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integrableObjects[kl]->getVel(aVel); |
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amass = integrableObjects[kl]->getMass(); |
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v_sqr = vx2 + vy2 + vz2; |
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kinetic += atoms[kl]->getMass() * v_sqr; |
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for(j=0; j<3; j++) |
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kinetic += amass*aVel[j]*aVel[j]; |
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|
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if( atoms[kl]->isDirectional() ){ |
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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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if (integrableObjects[kl]->isDirectional()){ |
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|
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integrableObjects[kl]->getJ( aJ ); |
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integrableObjects[kl]->getI( I ); |
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|
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if (integrableObjects[kl]->isLinear()) { |
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i = integrableObjects[kl]->linearAxis(); |
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j = (i+1)%3; |
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k = (i+2)%3; |
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kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k]; |
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} else { |
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for (j=0; j<3; j++) |
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kinetic += aJ[j]*aJ[j] / I[j][j]; |
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} |
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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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kinetic = kinetic * 0.5 / e_convert; |
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return kinetic; |
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int el, nSRI; |
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Molecule* molecules; |
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molecules = entry_plug->molecules; |
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nSRI = entry_plug->n_SRI; |
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molecules = info->molecules; |
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nSRI = info->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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potential_local += info->lrPot; |
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|
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for( el=0; el<entry_plug->n_mol; el++ ){ |
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for( el=0; el<info->n_mol; el++ ){ |
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potential_local += molecules[el].getPotential(); |
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} |
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potential = potential_local; |
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#endif // is_mpi |
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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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double Thermo::getTemperature(){ |
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
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const double kb = 1.9872156E-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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temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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return temperature; |
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} |
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double Thermo::getPressure(){ |
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// returns pressure in units amu*fs^-2*Ang^-1 |
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double Thermo::getVolume() { |
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|
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return info->boxVol; |
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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[3][3]; |
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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][0] + press[1][1] + press[2][2]) / 3.0; |
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|
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return pressure; |
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} |
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|
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> |
double Thermo::getPressureX() { |
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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[3][3]; |
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> |
double pressureX; |
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> |
|
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this->getPressureTensor(press); |
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|
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pressureX = p_convert * press[0][0]; |
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|
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return pressureX; |
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} |
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|
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double Thermo::getPressureY() { |
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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[3][3]; |
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double pressureY; |
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> |
|
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this->getPressureTensor(press); |
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|
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pressureY = p_convert * press[1][1]; |
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|
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return pressureY; |
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} |
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|
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double Thermo::getPressureZ() { |
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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[3][3]; |
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> |
double pressureZ; |
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|
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this->getPressureTensor(press); |
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|
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pressureZ = p_convert * press[2][2]; |
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|
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return pressureZ; |
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} |
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void Thermo::getPressureTensor(double press[3][3]){ |
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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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const double e_convert = 4.184e-4; |
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const double p_convert = 1.63882576e8; |
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double molmass; |
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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, p_sum, p_mol, virial; |
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< |
double theBox[3]; |
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double* tau; |
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int i, nMols; |
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> |
double p_local[9], p_global[9]; |
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> |
int i, j, k, 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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> |
nMols = info->n_mol; |
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molecules = info->molecules; |
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> |
//tau = info->tau; |
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|
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// use velocities of molecular centers of mass and molecular masses: |
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< |
p_local = 0.0; |
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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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< |
p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass; |
| 215 |
> |
|
| 216 |
> |
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]); |
| 220 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 221 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
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> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
| 223 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 224 |
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p_local[8] += molmass * (vcom[2] * vcom[2]); |
| 225 |
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} |
| 226 |
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|
| 227 |
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// Get total for entire system from MPI. |
| 228 |
+ |
|
| 229 |
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#ifdef IS_MPI |
| 230 |
< |
MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 230 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 231 |
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#else |
| 232 |
< |
p_sum = p_local; |
| 232 |
> |
for (i=0; i<9; i++) { |
| 233 |
> |
p_global[i] = p_local[i]; |
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> |
} |
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#endif // is_mpi |
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|
| 237 |
< |
virial = tau[0] + tau[4] + tau[8]; |
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< |
entry_plug->getBox(theBox); |
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> |
volume = this->getVolume(); |
| 238 |
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|
| 239 |
< |
p_mol = p_convert * (p_sum - virial*e_convert) / |
| 240 |
< |
(3.0 * theBox[0] * theBox[1]* theBox[2]); |
| 239 |
> |
for(i = 0; i < 3; i++) { |
| 240 |
> |
for (j = 0; j < 3; j++) { |
| 241 |
> |
k = 3*i + j; |
| 242 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
| 243 |
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|
| 244 |
< |
return p_mol; |
| 244 |
> |
} |
| 245 |
> |
} |
| 246 |
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} |
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|
| 248 |
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void Thermo::velocitize() { |
| 249 |
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|
| 250 |
< |
double x,y; |
| 251 |
< |
double vx, vy, vz; |
| 184 |
< |
double jx, jy, jz; |
| 185 |
< |
int i, vr, vd; // velocity randomizer loop counters |
| 250 |
> |
double aVel[3], aJ[3], I[3][3]; |
| 251 |
> |
int i, j, vr, vd; // velocity randomizer loop counters |
| 252 |
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double vdrift[3]; |
| 253 |
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double vbar; |
| 254 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 261 |
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int n_oriented; |
| 262 |
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int n_constraints; |
| 263 |
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|
| 264 |
< |
atoms = entry_plug->atoms; |
| 265 |
< |
n_atoms = entry_plug->n_atoms; |
| 266 |
< |
temperature = entry_plug->target_temp; |
| 267 |
< |
n_oriented = entry_plug->n_oriented; |
| 268 |
< |
n_constraints = entry_plug->n_constraints; |
| 264 |
> |
atoms = info->atoms; |
| 265 |
> |
n_atoms = info->n_atoms; |
| 266 |
> |
temperature = info->target_temp; |
| 267 |
> |
n_oriented = info->n_oriented; |
| 268 |
> |
n_constraints = info->n_constraints; |
| 269 |
|
|
| 270 |
< |
kebar = kb * temperature * (double)entry_plug->ndf / |
| 271 |
< |
( 2.0 * (double)entry_plug->ndfRaw ); |
| 270 |
> |
kebar = kb * temperature * (double)info->ndfRaw / |
| 271 |
> |
( 2.0 * (double)info->ndf ); |
| 272 |
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|
| 273 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 274 |
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|
| 276 |
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|
| 277 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
| 278 |
|
vbar = sqrt( av2 ); |
| 279 |
< |
|
| 214 |
< |
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
| 215 |
< |
|
| 279 |
> |
|
| 280 |
|
// picks random velocities from a gaussian distribution |
| 281 |
|
// centered on vbar |
| 282 |
|
|
| 283 |
< |
vx = vbar * gaussStream->getGaussian(); |
| 284 |
< |
vy = vbar * gaussStream->getGaussian(); |
| 285 |
< |
vz = vbar * gaussStream->getGaussian(); |
| 283 |
> |
for (j=0; j<3; j++) |
| 284 |
> |
aVel[j] = vbar * gaussStream->getGaussian(); |
| 285 |
> |
|
| 286 |
> |
atoms[vr]->setVel( aVel ); |
| 287 |
|
|
| 223 |
– |
atoms[vr]->set_vx( vx ); |
| 224 |
– |
atoms[vr]->set_vy( vy ); |
| 225 |
– |
atoms[vr]->set_vz( vz ); |
| 288 |
|
} |
| 289 |
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|
| 290 |
|
// Get the Center of Mass drift velocity. |
| 296 |
|
|
| 297 |
|
for(vd = 0; vd < n_atoms; vd++){ |
| 298 |
|
|
| 299 |
< |
vx = atoms[vd]->get_vx(); |
| 238 |
< |
vy = atoms[vd]->get_vy(); |
| 239 |
< |
vz = atoms[vd]->get_vz(); |
| 240 |
< |
|
| 241 |
< |
vx -= vdrift[0]; |
| 242 |
< |
vy -= vdrift[1]; |
| 243 |
< |
vz -= vdrift[2]; |
| 299 |
> |
atoms[vd]->getVel(aVel); |
| 300 |
|
|
| 301 |
< |
atoms[vd]->set_vx(vx); |
| 302 |
< |
atoms[vd]->set_vy(vy); |
| 303 |
< |
atoms[vd]->set_vz(vz); |
| 301 |
> |
for (j=0; j < 3; j++) |
| 302 |
> |
aVel[j] -= vdrift[j]; |
| 303 |
> |
|
| 304 |
> |
atoms[vd]->setVel( aVel ); |
| 305 |
|
} |
| 306 |
|
if( n_oriented ){ |
| 307 |
|
|
| 310 |
|
if( atoms[i]->isDirectional() ){ |
| 311 |
|
|
| 312 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 313 |
+ |
dAtom->getI( I ); |
| 314 |
+ |
|
| 315 |
+ |
for (j = 0 ; j < 3; j++) { |
| 316 |
|
|
| 317 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
| 318 |
< |
jx = vbar * gaussStream->getGaussian(); |
| 317 |
> |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
| 318 |
> |
aJ[j] = vbar * gaussStream->getGaussian(); |
| 319 |
|
|
| 320 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 321 |
< |
jy = vbar * gaussStream->getGaussian(); |
| 322 |
< |
|
| 323 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 264 |
< |
jz = vbar * gaussStream->getGaussian(); |
| 265 |
< |
|
| 266 |
< |
dAtom->setJx( jx ); |
| 267 |
< |
dAtom->setJy( jy ); |
| 268 |
< |
dAtom->setJz( jz ); |
| 320 |
> |
} |
| 321 |
> |
|
| 322 |
> |
dAtom->setJ( aJ ); |
| 323 |
> |
|
| 324 |
|
} |
| 325 |
|
} |
| 326 |
|
} |
| 329 |
|
void Thermo::getCOMVel(double vdrift[3]){ |
| 330 |
|
|
| 331 |
|
double mtot, mtot_local; |
| 332 |
+ |
double aVel[3], amass; |
| 333 |
|
double vdrift_local[3]; |
| 334 |
< |
int vd, n_atoms; |
| 334 |
> |
int vd, n_atoms, j; |
| 335 |
|
Atom** atoms; |
| 336 |
|
|
| 337 |
|
// We are very careless here with the distinction between n_atoms and n_local |
| 338 |
|
// We should really fix this before someone pokes an eye out. |
| 339 |
|
|
| 340 |
< |
n_atoms = entry_plug->n_atoms; |
| 341 |
< |
atoms = entry_plug->atoms; |
| 340 |
> |
n_atoms = info->n_atoms; |
| 341 |
> |
atoms = info->atoms; |
| 342 |
|
|
| 343 |
|
mtot_local = 0.0; |
| 344 |
|
vdrift_local[0] = 0.0; |
| 347 |
|
|
| 348 |
|
for(vd = 0; vd < n_atoms; vd++){ |
| 349 |
|
|
| 350 |
< |
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
| 351 |
< |
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
| 352 |
< |
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
| 350 |
> |
amass = atoms[vd]->getMass(); |
| 351 |
> |
atoms[vd]->getVel( aVel ); |
| 352 |
> |
|
| 353 |
> |
for(j = 0; j < 3; j++) |
| 354 |
> |
vdrift_local[j] += aVel[j] * amass; |
| 355 |
|
|
| 356 |
< |
mtot_local += atoms[vd]->getMass(); |
| 356 |
> |
mtot_local += amass; |
| 357 |
|
} |
| 358 |
|
|
| 359 |
|
#ifdef IS_MPI |
| 372 |
|
|
| 373 |
|
} |
| 374 |
|
|
| 375 |
+ |
void Thermo::getCOM(double COM[3]){ |
| 376 |
+ |
|
| 377 |
+ |
double mtot, mtot_local; |
| 378 |
+ |
double aPos[3], amass; |
| 379 |
+ |
double COM_local[3]; |
| 380 |
+ |
int i, n_atoms, j; |
| 381 |
+ |
Atom** atoms; |
| 382 |
+ |
|
| 383 |
+ |
// We are very careless here with the distinction between n_atoms and n_local |
| 384 |
+ |
// We should really fix this before someone pokes an eye out. |
| 385 |
+ |
|
| 386 |
+ |
n_atoms = info->n_atoms; |
| 387 |
+ |
atoms = info->atoms; |
| 388 |
+ |
|
| 389 |
+ |
mtot_local = 0.0; |
| 390 |
+ |
COM_local[0] = 0.0; |
| 391 |
+ |
COM_local[1] = 0.0; |
| 392 |
+ |
COM_local[2] = 0.0; |
| 393 |
+ |
|
| 394 |
+ |
for(i = 0; i < n_atoms; i++){ |
| 395 |
+ |
|
| 396 |
+ |
amass = atoms[i]->getMass(); |
| 397 |
+ |
atoms[i]->getPos( aPos ); |
| 398 |
+ |
|
| 399 |
+ |
for(j = 0; j < 3; j++) |
| 400 |
+ |
COM_local[j] += aPos[j] * amass; |
| 401 |
+ |
|
| 402 |
+ |
mtot_local += amass; |
| 403 |
+ |
} |
| 404 |
+ |
|
| 405 |
+ |
#ifdef IS_MPI |
| 406 |
+ |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 407 |
+ |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 408 |
+ |
#else |
| 409 |
+ |
mtot = mtot_local; |
| 410 |
+ |
for(i = 0; i < 3; i++) { |
| 411 |
+ |
COM[i] = COM_local[i]; |
| 412 |
+ |
} |
| 413 |
+ |
#endif |
| 414 |
+ |
|
| 415 |
+ |
for (i = 0; i < 3; i++) { |
| 416 |
+ |
COM[i] = COM[i] / mtot; |
| 417 |
+ |
} |
| 418 |
+ |
} |
