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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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double aVel[3], aJ[3], I[3][3]; |
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int j, 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 = info->n_atoms; |
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atoms = info->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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atoms[kl]->getVel(aVel); |
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amass = atoms[kl]->getMass(); |
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for (j=0; j < 3; j++) |
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kinetic += amass * aVel[j] * aVel[j]; |
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if( atoms[kl]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[kl]; |
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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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dAtom->getJ( aJ ); |
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dAtom->getI( I ); |
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for(j=0; j<3; j++) |
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kinetic += amass*aVel[j]*aVel[j]; |
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if (integrableObjects[kl]->isDirectional()){ |
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integrableObjects[kl]->getJ( aJ ); |
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integrableObjects[kl]->getI( I ); |
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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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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)info->ndf * kb ); |
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return temperature; |
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} |
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double Thermo::getEnthalpy() { |
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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[3][3]; |
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u = this->getTotalE(); |
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this->getPressureTensor(press); |
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p = (press[0][0] + press[1][1] + press[2][2]) / 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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void Thermo::velocitize() { |
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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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n_oriented = info->n_oriented; |
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n_constraints = info->n_constraints; |
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kebar = kb * temperature * (double)info->ndf / |
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( 2.0 * (double)info->ndfRaw ); |
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kebar = kb * temperature * (double)info->ndfRaw / |
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( 2.0 * (double)info->ndf ); |
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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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// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
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// picks random velocities from a gaussian distribution |
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// centered on vbar |
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} |
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} |
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void Thermo::getCOM(double COM[3]){ |
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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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// 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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n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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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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for(i = 0; i < n_atoms; i++){ |
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amass = atoms[i]->getMass(); |
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atoms[i]->getPos( aPos ); |
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for(j = 0; j < 3; j++) |
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COM_local[j] += aPos[j] * amass; |
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mtot_local += amass; |
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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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for (i = 0; i < 3; i++) { |
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COM[i] = COM[i] / mtot; |
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} |
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} |
