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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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nAtoms = info->n_atoms; |
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// check for constraints |
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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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tStats = new Thermo(info); |
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// initialize the forces before the first step |
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std::cerr << "Before initial Force calc\n"; |
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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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calcForce(1, 1); |
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constrainB(); |
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std::cerr << "premove done\n"; |
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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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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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currReset += resetTime; |
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} |
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} |
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std::cerr << "done with time = " << info->getTime() << "\n"; |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "successfully took a time step."); |
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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->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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} |
