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#include <iostream> |
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#include <cstdlib> |
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#include <cmath> |
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#include <stdlib.h> |
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#include <math.h> |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#include <unistd.h> |
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#endif //is_mpi |
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#ifdef PROFILE |
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#include "mdProfile.hpp" |
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#endif // profile |
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|
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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if (info->the_integrator != NULL){ |
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delete info->the_integrator; |
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} |
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info->the_integrator = this; |
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nAtoms = info->n_atoms; |
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|
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template<typename T> void Integrator<T>::integrate(void){ |
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int i, j; // loop counters |
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double runTime = info->run_time; |
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double sampleTime = info->sampleTime; |
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double statusTime = info->statusTime; |
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double thermalTime = info->thermalTime; |
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double resetTime = info->resetTime; |
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|
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double currSample; |
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double currThermal; |
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double currStatus; |
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double currReset; |
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int calcPot, calcStress; |
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int isError; |
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tStats = new Thermo(info); |
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statOut = new StatWriter(info); |
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dumpOut = new DumpWriter(info); |
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atoms = info->atoms; |
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DirectionalAtom* dAtom; |
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dt = info->dt; |
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dt2 = 0.5 * dt; |
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readyCheck(); |
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|
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// initialize the forces before the first step |
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calcForce(1, 1); |
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// myFF->doForces(1,1); |
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if (nConstrained){ |
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preMove(); |
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constrainA(); |
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calcForce(1, 1); |
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constrainB(); |
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} |
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|
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if (info->setTemp){ |
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thermalize(); |
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} |
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|
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calcPot = 0; |
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calcStress = 0; |
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currSample = sampleTime; |
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currThermal = thermalTime; |
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currStatus = statusTime; |
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|
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calcPot = 0; |
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calcStress = 0; |
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currSample = sampleTime + info->getTime(); |
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currThermal = thermalTime+ info->getTime(); |
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currStatus = statusTime + info->getTime(); |
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>>>>>>> 1.18 |
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currReset = resetTime + info->getTime(); |
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dumpOut->writeDump(info->getTime()); |
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statOut->writeStat(info->getTime()); |
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readyCheck(); |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "The integrator is ready to go."); |
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calcStress = 1; |
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} |
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#ifdef PROFILE |
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startProfile( pro1 ); |
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#endif |
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|
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integrateStep(calcPot, calcStress); |
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#ifdef PROFILE |
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endProfile( pro1 ); |
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|
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startProfile( pro2 ); |
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#endif // profile |
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|
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info->incrTime(dt); |
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if (info->setTemp){ |
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} |
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if (info->getTime() >= currStatus){ |
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statOut->writeStat(info->getTime()); |
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calcPot = 0; |
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statOut->writeStat(info->getTime()); |
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calcPot = 0; |
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calcStress = 0; |
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currStatus += statusTime; |
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} |
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} |
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if (info->resetIntegrator){ |
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if (info->getTime() >= currReset){ |
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this->resetIntegrator(); |
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currReset += resetTime; |
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} |
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} |
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|
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#ifdef PROFILE |
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endProfile( pro2 ); |
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#endif //profile |
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|
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "successfully took a time step."); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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dumpOut->writeFinal(info->getTime()); |
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|
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// write the last frame |
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dumpOut->writeDump(info->getTime()); |
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|
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delete dumpOut; |
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delete statOut; |
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} |
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template<typename T> void Integrator<T>::integrateStep(int calcPot, |
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int calcStress){ |
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// Position full step, and velocity half step |
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|
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#ifdef PROFILE |
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startProfile(pro3); |
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#endif //profile |
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|
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preMove(); |
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#ifdef PROFILE |
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endProfile(pro3); |
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|
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startProfile(pro4); |
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#endif // profile |
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|
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moveA(); |
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if (nConstrained){ |
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constrainA(); |
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} |
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#ifdef PROFILE |
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endProfile(pro4); |
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|
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startProfile(pro5); |
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#endif//profile |
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#ifdef IS_MPI |
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MPIcheckPoint(); |
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#endif // is_mpi |
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#ifdef PROFILE |
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endProfile( pro5 ); |
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startProfile( pro6 ); |
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#endif //profile |
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|
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// finish the velocity half step |
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moveB(); |
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if (nConstrained){ |
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constrainB(); |
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} |
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#ifdef PROFILE |
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endProfile(pro6); |
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#endif // profile |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "Succesful moveB\n"); |
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int i, j; |
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DirectionalAtom* dAtom; |
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double Tb[3], ji[3]; |
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double A[3][3], I[3][3]; |
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double angle; |
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double vel[3], pos[3], frc[3]; |
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double mass; |
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for (j = 0; j < 3; j++) |
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ji[j] += (dt2 * Tb[j]) * eConvert; |
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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this->rotationPropagation( dAtom, ji ); |
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dAtom->getA(A); |
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dAtom->getI(I); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate(1, 2, angle, ji, A); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate(2, 0, angle, ji, A); |
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|
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// rotate about the z-axis |
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angle = dt * ji[2] / I[2][2]; |
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this->rotate(0, 1, angle, ji, A); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate(2, 0, angle, ji, A); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate(1, 2, angle, ji, A); |
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|
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dAtom->setJ(ji); |
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dAtom->setA(A); |
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} |
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} |
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|
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if (nConstrained){ |
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constrainA(); |
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} |
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} |
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if (atoms[i]->isDirectional()){ |
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dAtom = (DirectionalAtom *) atoms[i]; |
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// get and convert the torque to body frame |
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// get and convert the torque to body frame |
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dAtom->getTrq(Tb); |
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dAtom->lab2Body(Tb); |
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dAtom->setJ(ji); |
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} |
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} |
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|
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if (nConstrained){ |
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constrainB(); |
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} |
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} |
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template<typename T> void Integrator<T>::preMove(void){ |
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} |
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template<typename T> void Integrator<T>::constrainA(){ |
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int i, j, k; |
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int i, j; |
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int done; |
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double posA[3], posB[3]; |
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double velA[3], velB[3]; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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template<typename T> void Integrator<T>::constrainB(void){ |
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int i, j, k; |
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int i, j; |
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int done; |
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double posA[3], posB[3]; |
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double velA[3], velB[3]; |
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int a, b, ax, ay, az, bx, by, bz; |
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double rma, rmb; |
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double dx, dy, dz; |
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double rabsq, pabsq, rvab; |
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double diffsq; |
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double rvab; |
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double gab; |
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int iteration; |
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} |
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} |
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|
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template<typename T> void Integrator<T>::rotationPropagation |
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( DirectionalAtom* dAtom, double ji[3] ){ |
691 |
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|
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double angle; |
693 |
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double A[3][3], I[3][3]; |
694 |
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|
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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|
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dAtom->getA(A); |
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dAtom->getI(I); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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|
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// rotate about the z-axis |
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angle = dt * ji[2] / I[2][2]; |
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this->rotate( 0, 1, angle, ji, A); |
712 |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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|
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// rotate about the x-axis |
718 |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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|
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dAtom->setA( A ); |
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} |
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|
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template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
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double angle, double ji[3], |
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double A[3][3]){ |
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} |
787 |
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} |
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|
789 |
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// rotate the Rotation matrix acording to: |
789 |
> |
// rotate the Rotation matrix acording to: |
790 |
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// A[][] = A[][] * transpose(rot[][]) |
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|
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|
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template<typename T> void Integrator<T>::thermalize(){ |
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tStats->velocitize(); |
813 |
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} |
814 |
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|
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template<typename T> double Integrator<T>::getConservedQuantity(void){ |
816 |
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return tStats->getTotalE(); |
817 |
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} |
818 |
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template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
819 |
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//By default, return a null string |
820 |
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//The reason we use string instead of char* is that if we use char*, we will |
821 |
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//return a pointer point to local variable which might cause problem |
822 |
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return string(); |
823 |
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} |