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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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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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|
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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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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n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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|
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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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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molecules = info->molecules; |
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nSRI = info->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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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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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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|
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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::getVolume() { |
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return entry_plug->boxVol; |
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return info->boxVol; |
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} |
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double Thermo::getPressure() { |
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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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|
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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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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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int i, j, k, l, nMols; |
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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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for (i=0; i < 9; i++) { |
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for(i = 0; i < 3; i++) { |
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for (j = 0; j < 3; j++) { |
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k = 3*i + j; |
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press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume; |
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press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
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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::velocitize() { |
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|
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double x,y; |
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double aVel[3], aJ[3], I[3][3]; |
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int i, j, vr, vd; // velocity randomizer loop counters |
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double vdrift[3]; |
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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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atoms = info->atoms; |
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n_atoms = info->n_atoms; |
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temperature = info->target_temp; |
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n_oriented = info->n_oriented; |
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n_constraints = info->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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kebar = kb * temperature * (double)info->ndfRaw / |
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( 2.0 * (double)info->ndf ); |
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|
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for(vr = 0; vr < n_atoms; vr++){ |
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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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n_atoms = info->n_atoms; |
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atoms = info->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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|
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} |
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|
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void Thermo::getCOM(double COM[3]){ |
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|
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double mtot, mtot_local; |
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double aPos[3], amass; |
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double COM_local[3]; |
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int i, n_atoms, j; |
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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 = info->n_atoms; |
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atoms = info->atoms; |
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|
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mtot_local = 0.0; |
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COM_local[0] = 0.0; |
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COM_local[1] = 0.0; |
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COM_local[2] = 0.0; |
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|
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for(i = 0; i < n_atoms; i++){ |
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|
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amass = atoms[i]->getMass(); |
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atoms[i]->getPos( aPos ); |
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|
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for(j = 0; j < 3; j++) |
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COM_local[j] += aPos[j] * amass; |
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|
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mtot_local += amass; |
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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(COM_local,COM,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(i = 0; i < 3; i++) { |
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COM[i] = COM_local[i]; |
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} |
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#endif |
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|
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for (i = 0; i < 3; i++) { |
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COM[i] = COM[i] / mtot; |
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} |
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} |