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#include <math.h> |
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mmeineke |
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#include <iostream> |
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using namespace std; |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
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#include "Thermo.hpp" |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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#include "MatVec3.h" |
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#ifdef IS_MPI |
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#define __C |
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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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|
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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mmeineke |
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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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mmeineke |
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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Thermo::~Thermo(){ |
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delete gaussStream; |
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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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gezelter |
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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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tim |
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int i, j, k, kl; |
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mmeineke |
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double kinetic_global; |
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tim |
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vector<StuntDouble *> integrableObjects = info->integrableObjects; |
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mmeineke |
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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tim |
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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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gezelter |
608 |
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tim |
1113 |
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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tim |
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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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tim |
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} |
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gezelter |
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} |
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mmeineke |
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} |
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#ifdef IS_MPI |
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mmeineke |
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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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mmeineke |
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kinetic = kinetic_global; |
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#endif //is_mpi |
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gezelter |
1125 |
|
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mmeineke |
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kinetic = kinetic * 0.5 / e_convert; |
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return kinetic; |
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} |
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double Thermo::getPotential(){ |
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chuckv |
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double potential_local; |
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mmeineke |
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double potential; |
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int el, nSRI; |
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mmeineke |
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Molecule* molecules; |
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mmeineke |
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mmeineke |
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molecules = info->molecules; |
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nSRI = info->n_SRI; |
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mmeineke |
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chuckv |
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potential_local = 0.0; |
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chuckv |
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potential = 0.0; |
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mmeineke |
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potential_local += info->lrPot; |
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mmeineke |
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|
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mmeineke |
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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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mmeineke |
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} |
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// Get total potential for entire system from MPI. |
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#ifdef IS_MPI |
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MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
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MPI_SUM, MPI_COMM_WORLD); |
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chuckv |
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#else |
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potential = potential_local; |
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#endif // is_mpi |
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return potential; |
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} |
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double Thermo::getTotalE(){ |
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double total; |
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total = this->getKinetic() + this->getPotential(); |
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return total; |
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} |
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gezelter |
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double Thermo::getTemperature(){ |
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tim |
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const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
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gezelter |
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double temperature; |
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tim |
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mmeineke |
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temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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mmeineke |
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return temperature; |
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} |
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gezelter |
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double Thermo::getVolume() { |
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gezelter |
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mmeineke |
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return info->boxVol; |
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} |
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gezelter |
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double Thermo::getPressure() { |
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gezelter |
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gezelter |
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// Relies on the calculation of the full molecular pressure tensor |
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const double p_convert = 1.63882576e8; |
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gezelter |
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double press[3][3]; |
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gezelter |
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double pressure; |
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this->getPressureTensor(press); |
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gezelter |
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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gezelter |
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return pressure; |
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} |
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mmeineke |
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double Thermo::getPressureX() { |
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gezelter |
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mmeineke |
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// Relies on the calculation of the full molecular pressure tensor |
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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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this->getPressureTensor(press); |
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pressureX = p_convert * press[0][0]; |
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return pressureX; |
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} |
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double Thermo::getPressureY() { |
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// Relies on the calculation of the full molecular pressure tensor |
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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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this->getPressureTensor(press); |
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pressureY = p_convert * press[1][1]; |
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return pressureY; |
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} |
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double Thermo::getPressureZ() { |
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// Relies on the calculation of the full molecular pressure tensor |
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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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this->getPressureTensor(press); |
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pressureZ = p_convert * press[2][2]; |
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return pressureZ; |
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} |
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gezelter |
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void Thermo::getPressureTensor(double press[3][3]){ |
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gezelter |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
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gezelter |
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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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mmeineke |
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gezelter |
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const double e_convert = 4.184e-4; |
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gezelter |
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double molmass, volume; |
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tim |
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double vcom[3], pcom[3], fcom[3], scaled[3]; |
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gezelter |
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double p_local[9], p_global[9]; |
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mmeineke |
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int i, j, k, nMols; |
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gezelter |
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Molecule* molecules; |
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mmeineke |
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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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gezelter |
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// use velocities of molecular centers of mass and molecular masses: |
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gezelter |
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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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gezelter |
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tim |
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for (i=0; i < info->integrableObjects.size(); i++) { |
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gezelter |
483 |
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tim |
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molmass = info->integrableObjects[i]->getMass(); |
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info->integrableObjects[i]->getVel(vcom); |
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info->integrableObjects[i]->getPos(pcom); |
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info->integrableObjects[i]->getFrc(fcom); |
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matVecMul3(info->HmatInv, pcom, scaled); |
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for(j=0; j<3; j++) |
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scaled[j] -= roundMe(scaled[j]); |
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// calc the wrapped real coordinates from the wrapped scaled coordinates |
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matVecMul3(info->Hmat, scaled, pcom); |
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p_local[0] += molmass * (vcom[0] * vcom[0]) + fcom[0]*pcom[0]*eConvert; |
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p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert; |
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p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert; |
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p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert; |
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p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert; |
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p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert; |
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p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert; |
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p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert; |
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p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert; |
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gezelter |
468 |
} |
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// Get total for entire system from MPI. |
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chuckv |
479 |
|
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gezelter |
468 |
#ifdef IS_MPI |
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gezelter |
483 |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
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gezelter |
468 |
#else |
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gezelter |
483 |
for (i=0; i<9; i++) { |
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p_global[i] = p_local[i]; |
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} |
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gezelter |
468 |
#endif // is_mpi |
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gezelter |
611 |
volume = this->getVolume(); |
258 |
gezelter |
468 |
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gezelter |
588 |
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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tim |
1131 |
press[i][j] = p_global[k] / volume; |
263 |
mmeineke |
614 |
|
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gezelter |
588 |
} |
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gezelter |
483 |
} |
266 |
mmeineke |
377 |
} |
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void Thermo::velocitize() { |
269 |
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gezelter |
608 |
double aVel[3], aJ[3], I[3][3]; |
271 |
tim |
1127 |
int i, j, l, m, n, vr, vd; // velocity randomizer loop counters |
272 |
chuckv |
403 |
double vdrift[3]; |
273 |
mmeineke |
377 |
double vbar; |
274 |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
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double av2; |
276 |
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double kebar; |
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double temperature; |
278 |
tim |
1127 |
int nobj; |
279 |
mmeineke |
377 |
|
280 |
tim |
1127 |
nobj = info->integrableObjects.size(); |
281 |
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282 |
mmeineke |
614 |
temperature = info->target_temp; |
283 |
mmeineke |
377 |
|
284 |
tim |
763 |
kebar = kb * temperature * (double)info->ndfRaw / |
285 |
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( 2.0 * (double)info->ndf ); |
286 |
chuckv |
403 |
|
287 |
tim |
1127 |
for(vr = 0; vr < nobj; vr++){ |
288 |
mmeineke |
377 |
|
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// uses equipartition theory to solve for vbar in angstrom/fs |
290 |
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291 |
tim |
1127 |
av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass(); |
292 |
mmeineke |
377 |
vbar = sqrt( av2 ); |
293 |
mmeineke |
853 |
|
294 |
mmeineke |
377 |
// picks random velocities from a gaussian distribution |
295 |
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// centered on vbar |
296 |
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297 |
gezelter |
608 |
for (j=0; j<3; j++) |
298 |
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aVel[j] = vbar * gaussStream->getGaussian(); |
299 |
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300 |
tim |
1127 |
info->integrableObjects[vr]->setVel( aVel ); |
301 |
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302 |
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if(info->integrableObjects[vr]->isDirectional()){ |
303 |
mmeineke |
377 |
|
304 |
tim |
1127 |
info->integrableObjects[vr]->getI( I ); |
305 |
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306 |
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if (info->integrableObjects[vr]->isLinear()) { |
307 |
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308 |
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l= info->integrableObjects[vr]->linearAxis(); |
309 |
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m = (l+1)%3; |
310 |
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n = (l+2)%3; |
311 |
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312 |
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aJ[l] = 0.0; |
313 |
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vbar = sqrt( 2.0 * kebar * I[m][m] ); |
314 |
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aJ[m] = vbar * gaussStream->getGaussian(); |
315 |
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vbar = sqrt( 2.0 * kebar * I[n][n] ); |
316 |
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aJ[n] = vbar * gaussStream->getGaussian(); |
317 |
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318 |
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} else { |
319 |
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for (j = 0 ; j < 3; j++) { |
320 |
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vbar = sqrt( 2.0 * kebar * I[j][j] ); |
321 |
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aJ[j] = vbar * gaussStream->getGaussian(); |
322 |
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} |
323 |
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} // else isLinear |
324 |
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325 |
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info->integrableObjects[vr]->setJ( aJ ); |
326 |
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327 |
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}//isDirectional |
328 |
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329 |
mmeineke |
377 |
} |
330 |
chuckv |
401 |
|
331 |
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// Get the Center of Mass drift velocity. |
332 |
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|
333 |
chuckv |
403 |
getCOMVel(vdrift); |
334 |
mmeineke |
377 |
|
335 |
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// Corrects for the center of mass drift. |
336 |
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// sums all the momentum and divides by total mass. |
337 |
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338 |
tim |
1127 |
for(vd = 0; vd < nobj; vd++){ |
339 |
mmeineke |
377 |
|
340 |
tim |
1127 |
info->integrableObjects[vd]->getVel(aVel); |
341 |
gezelter |
608 |
|
342 |
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for (j=0; j < 3; j++) |
343 |
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aVel[j] -= vdrift[j]; |
344 |
chuckv |
401 |
|
345 |
tim |
1127 |
info->integrableObjects[vd]->setVel( aVel ); |
346 |
mmeineke |
377 |
} |
347 |
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348 |
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} |
349 |
chuckv |
401 |
|
350 |
chuckv |
403 |
void Thermo::getCOMVel(double vdrift[3]){ |
351 |
chuckv |
401 |
|
352 |
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double mtot, mtot_local; |
353 |
gezelter |
608 |
double aVel[3], amass; |
354 |
chuckv |
401 |
double vdrift_local[3]; |
355 |
tim |
1127 |
int vd, j; |
356 |
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int nobj; |
357 |
chuckv |
401 |
|
358 |
tim |
1127 |
nobj = info->integrableObjects.size(); |
359 |
chuckv |
401 |
|
360 |
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mtot_local = 0.0; |
361 |
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vdrift_local[0] = 0.0; |
362 |
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vdrift_local[1] = 0.0; |
363 |
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vdrift_local[2] = 0.0; |
364 |
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|
365 |
tim |
1127 |
for(vd = 0; vd < nobj; vd++){ |
366 |
chuckv |
401 |
|
367 |
tim |
1127 |
amass = info->integrableObjects[vd]->getMass(); |
368 |
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info->integrableObjects[vd]->getVel( aVel ); |
369 |
gezelter |
608 |
|
370 |
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for(j = 0; j < 3; j++) |
371 |
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|
vdrift_local[j] += aVel[j] * amass; |
372 |
chuckv |
401 |
|
373 |
gezelter |
608 |
mtot_local += amass; |
374 |
chuckv |
401 |
} |
375 |
|
|
|
376 |
|
|
#ifdef IS_MPI |
377 |
mmeineke |
447 |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
378 |
|
|
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
379 |
chuckv |
401 |
#else |
380 |
|
|
mtot = mtot_local; |
381 |
|
|
for(vd = 0; vd < 3; vd++) { |
382 |
|
|
vdrift[vd] = vdrift_local[vd]; |
383 |
|
|
} |
384 |
|
|
#endif |
385 |
|
|
|
386 |
|
|
for (vd = 0; vd < 3; vd++) { |
387 |
|
|
vdrift[vd] = vdrift[vd] / mtot; |
388 |
|
|
} |
389 |
|
|
|
390 |
|
|
} |
391 |
|
|
|
392 |
tim |
763 |
void Thermo::getCOM(double COM[3]){ |
393 |
|
|
|
394 |
|
|
double mtot, mtot_local; |
395 |
|
|
double aPos[3], amass; |
396 |
|
|
double COM_local[3]; |
397 |
tim |
1127 |
int i, j; |
398 |
|
|
int nobj; |
399 |
tim |
763 |
|
400 |
|
|
mtot_local = 0.0; |
401 |
|
|
COM_local[0] = 0.0; |
402 |
|
|
COM_local[1] = 0.0; |
403 |
|
|
COM_local[2] = 0.0; |
404 |
tim |
1127 |
|
405 |
|
|
nobj = info->integrableObjects.size(); |
406 |
|
|
for(i = 0; i < nobj; i++){ |
407 |
tim |
763 |
|
408 |
tim |
1127 |
amass = info->integrableObjects[i]->getMass(); |
409 |
|
|
info->integrableObjects[i]->getPos( aPos ); |
410 |
tim |
763 |
|
411 |
|
|
for(j = 0; j < 3; j++) |
412 |
|
|
COM_local[j] += aPos[j] * amass; |
413 |
|
|
|
414 |
|
|
mtot_local += amass; |
415 |
|
|
} |
416 |
|
|
|
417 |
|
|
#ifdef IS_MPI |
418 |
|
|
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
419 |
|
|
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
420 |
|
|
#else |
421 |
|
|
mtot = mtot_local; |
422 |
|
|
for(i = 0; i < 3; i++) { |
423 |
|
|
COM[i] = COM_local[i]; |
424 |
|
|
} |
425 |
|
|
#endif |
426 |
|
|
|
427 |
|
|
for (i = 0; i < 3; i++) { |
428 |
|
|
COM[i] = COM[i] / mtot; |
429 |
|
|
} |
430 |
|
|
} |
431 |
tim |
1127 |
|
432 |
|
|
void Thermo::removeCOMdrift() { |
433 |
|
|
double vdrift[3], aVel[3]; |
434 |
|
|
int vd, j, nobj; |
435 |
|
|
|
436 |
|
|
nobj = info->integrableObjects.size(); |
437 |
|
|
|
438 |
|
|
// Get the Center of Mass drift velocity. |
439 |
|
|
|
440 |
|
|
getCOMVel(vdrift); |
441 |
|
|
|
442 |
|
|
// Corrects for the center of mass drift. |
443 |
|
|
// sums all the momentum and divides by total mass. |
444 |
|
|
|
445 |
|
|
for(vd = 0; vd < nobj; vd++){ |
446 |
|
|
|
447 |
|
|
info->integrableObjects[vd]->getVel(aVel); |
448 |
|
|
|
449 |
|
|
for (j=0; j < 3; j++) |
450 |
|
|
aVel[j] -= vdrift[j]; |
451 |
|
|
|
452 |
|
|
info->integrableObjects[vd]->setVel( aVel ); |
453 |
|
|
} |
454 |
gezelter |
1133 |
} |