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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 "brains/Thermo.hpp" |
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#include "primitives/SRI.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "math/MatVec3.h" |
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#include "utils/OOPSEConstant.hpp" |
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#ifdef IS_MPI |
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#define __C |
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#include "brains/mpiSimulation.hpp" |
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#endif // is_mpi |
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namespace oopse { |
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Thermo::Thermo(SimInfo *the_info) { info = the_info; } |
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Thermo::~Thermo() { } |
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double Thermo::getKinetic() { |
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const double e_convert = |
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4.184E - 4; // convert kcal/mol -> (amu A^2)/fs^2 |
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double kinetic; |
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double amass; |
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double aVel[3], |
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aJ[3], |
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I[3][3]; |
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int i, |
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j, |
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k, |
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kl; |
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SimInfo::MoleculeIterator miter; |
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std::vector<StuntDouble*>::iterator iiter; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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double mass; |
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Vector3d vel; |
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Vector3d angMom; |
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Mat3x3d I; |
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int i; |
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int j; |
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int k; |
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double kinetic = 0.0; |
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double kinetic_global = 0.0; |
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for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) { |
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for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(iiter)) { |
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double kinetic_global; |
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vector<StuntDouble *>integrableObjects = info->integrableObjects; |
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double mass = integrableObject->getMass(); |
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Vector3d vel = integrableObject->getVel(); |
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]); |
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for( kl = 0; kl < integrableObjects.size(); kl++ ) { |
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aVel = integrableObjects[kl]->getVel(); |
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amass = integrableObjects[kl]->getMass(); |
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if (integrableObject->isDirectional()) { |
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angMom = integrableObject->getJ(); |
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I = integrableObject->getI(); |
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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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aJ = integrableObjects[kl]->getJ(); |
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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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if (integrableObject->isLinear()) { |
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i = integrableObject->linearAxis(); |
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j = (i + 1) % 3; |
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k = (i + 2) % 3; |
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kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k); |
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} else { |
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kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1) |
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+ angMom[2]*angMom[2]/I(2, 2); |
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} |
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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, MPI_SUM, |
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#endif //is_mpi |
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kinetic = kinetic * 0.5 / e_convert; |
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kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert; |
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return kinetic; |
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} |
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double Thermo::getPotential() { |
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double potential_local; |
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double potential; |
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int el, |
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nSRI; |
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Molecule *molecules; |
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double potential = 0.0; |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL]; |
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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 += info->lrPot; |
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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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SimInfo::MoleculeIterator i; |
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Molecule* mol; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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potential_local += mol->getPotential(); |
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} |
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// Get total potential for entire system from MPI. |
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} |
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double Thermo::getTemperature() { |
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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 |
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= ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
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double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb ); |
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return temperature; |
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} |
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double Thermo::getVolume() { return info->boxVol; } |
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double Thermo::getVolume() { |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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return curSnapshot->getVolume(); |
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} |
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double Thermo::getPressure() { |
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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 pressure; |
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this->getPressureTensor(press); |
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Mat3x3d tensor; |
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double pressure; |
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
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this->getPressureTensor(tensor); |
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pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0; |
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return pressure; |
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} |
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double Thermo::getPressureX() { |
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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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void Thermo::getPressureTensor(double press[3][3]) { |
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void Thermo::getPressureTensor(Mat3x3d pressureTensor) { |
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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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Mat3x3d p_local(0.0); |
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Mat3x3d p_global(0.0); |
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double molmass, |
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volume; |
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double vcom[3]; |
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double p_local[9], |
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p_global[9]; |
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int i, |
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j, |
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k; |
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SimInfo::MoleculeIterator i; |
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std::vector<StuntDouble*>::iterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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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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double mass = integrableObject->getMass(); |
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Vector3d vcom = integrableObject->getVel(); |
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p_local += mass * outProduct(vcom, vcom); |
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} |
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} |
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// use velocities of integrableObjects and their masses: |
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for( i = 0; i < info->integrableObjects.size(); i++ ) { |
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molmass = info->integrableObjects[i]->getMass(); |
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vcom = info->integrableObjects[i]->getVel(); |
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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]); |
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p_local[4] += molmass * (vcom[1] * vcom[1]); |
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p_local[5] += molmass * (vcom[1] * vcom[2]); |
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p_local[6] += molmass * (vcom[2] * vcom[0]); |
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p_local[7] += molmass * (vcom[2] * vcom[1]); |
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p_local[8] += molmass * (vcom[2] * vcom[2]); |
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} |
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// Get total for entire system from MPI. |
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#ifdef IS_MPI |
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MPI_Allreduce(p_local, p_global, 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
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#else |
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for( i = 0; i < 9; i++ ) { |
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p_global[i] = p_local[i]; |
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} |
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p_global = p_local; |
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#endif // is_mpi |
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volume = this->getVolume(); |
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double volume = this->getVolume(); |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Mat3x3d tau = curSnapshot->statData.getTau(); |
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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 |
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[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
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} |
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} |
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pressureTensor = p_global + OOPSEConstant::energyConvert/volume * tau; |
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} |
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} //end namespace oopse |
