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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 kinetic; |
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double amass; |
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double aVel[3], aJ[3], I[3][3]; |
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int j, kl; |
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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 = 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 += aJ[j]*aJ[j] / I[j][j]; |
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} |
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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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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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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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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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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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