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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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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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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 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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// initialize the forces before the first step |
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calcForce(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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if (info->setTemp){ |
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thermalize(); |
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} |
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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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MPIcheckPoint(); |
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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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#endif // is_mpi |
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} |
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dumpOut->writeFinal(info->getTime()); |
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// write the last frame |
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dumpOut->writeDump(info->getTime()); |
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delete dumpOut; |
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delete statOut; |
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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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} |
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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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} |
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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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dAtom->getA(A); |
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dAtom->getI(I); |
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// rotate about the x-axis |
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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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this->rotate( 1, 2, angle, ji, A ); |
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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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// 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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// 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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// 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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dAtom->setA( A ); |
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dAtom->setA( A ); |
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} |
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template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
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} |
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} |
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// rotate the Rotation matrix acording to: |
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// rotate the Rotation matrix acording to: |
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// A[][] = A[][] * transpose(rot[][]) |
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template<typename T> double Integrator<T>::getConservedQuantity(void){ |
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return tStats->getTotalE(); |
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} |
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template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
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//By default, return a null string |
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//The reason we use string instead of char* is that if we use char*, we will |
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//return a pointer point to local variable which might cause problem |
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return string(); |
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} |
