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mmeineke |
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#include <iostream> |
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#include <cstdlib> |
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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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#include "Integrator.hpp" |
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#include "simError.h" |
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Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
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info = theInfo; |
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myFF = the_ff; |
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isFirst = 1; |
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molecules = info->molecules; |
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nMols = info->n_mol; |
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// give a little love back to the SimInfo object |
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if( info->the_integrator != NULL ) delete info->the_integrator; |
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info->the_integrator = this; |
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nAtoms = info->n_atoms; |
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// check for constraints |
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constrainedA = NULL; |
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constrainedB = NULL; |
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constrainedDsqr = NULL; |
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moving = NULL; |
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moved = NULL; |
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prePos = NULL; |
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nConstrained = 0; |
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checkConstraints(); |
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} |
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Integrator::~Integrator() { |
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if( nConstrained ){ |
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delete[] constrainedA; |
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delete[] constrainedB; |
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delete[] constrainedDsqr; |
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delete[] moving; |
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delete[] moved; |
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delete[] prePos; |
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k |
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} |
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} |
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void Integrator::checkConstraints( void ){ |
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isConstrained = 0; |
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[info->n_SRI]; |
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nConstrained = 0; |
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int constrained = 0; |
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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theArray = (SRI**) molecules[i].getMyBonds(); |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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theArray = (SRI**) molecules[i].getMyBends(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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} |
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if(nConstrained > 0){ |
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isConstrained = 1; |
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if(constrainedA != NULL ) delete[] constrainedA; |
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if(constrainedB != NULL ) delete[] constrainedB; |
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if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
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constrainedA = new int[nConstrained]; |
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constrainedB = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
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for( int i = 0; i < nConstrained; i++){ |
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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} |
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// save oldAtoms to check for lode balanceing later on. |
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oldAtoms = nAtoms; |
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moving = new int[nAtoms]; |
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moved = new int[nAtoms]; |
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prePos = new double[nAtoms*3]; |
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} |
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delete[] temp_con; |
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} |
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void Integrator::integrate( void ){ |
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int i, j; // loop counters |
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double kE = 0.0; // the kinetic energy |
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double rot_kE; |
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double trans_kE; |
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int tl; // the time loop conter |
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double dt2; // half the dt |
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double vx, vy, vz; // the velocities |
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double vx2, vy2, vz2; // the square of the velocities |
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double rx, ry, rz; // the postitions |
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double ji[3]; // the body frame angular momentum |
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double jx2, jy2, jz2; // the square of the angular momentums |
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double Tb[3]; // torque in the body frame |
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double angle; // the angle through which to rotate the rotation matrix |
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double A[3][3]; // the rotation matrix |
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double press[9]; |
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double dt = info->dt; |
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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 currSample; |
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double currThermal; |
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double currStatus; |
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double currTime; |
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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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e_out = new StatWriter( info ); |
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dump_out = new DumpWriter( info ); |
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Atom** atoms = info->atoms; |
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DirectionalAtom* dAtom; |
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dt2 = 0.5 * dt; |
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// initialize the forces before the first step |
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myFF->doForces(1,1); |
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if( info->setTemp ){ |
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tStats->velocitize(); |
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} |
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dump_out->writeDump( 0.0 ); |
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e_out->writeStat( 0.0 ); |
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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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currTime = 0.0;; |
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while( currTime < runTime ){ |
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if( (currTime+dt) >= currStatus ){ |
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calcPot = 1; |
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calcStress = 1; |
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} |
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integrateStep( calcPot, calcStress ); |
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currTime += dt; |
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if( info->setTemp ){ |
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if( currTime >= currThermal ){ |
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tStats->velocitize(); |
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currThermal += thermalTime; |
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} |
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} |
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if( currTime >= currSample ){ |
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dump_out->writeDump( currTime ); |
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currSample += sampleTime; |
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} |
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if( currTime >= currStatus ){ |
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e_out->writeStat( time * dt ); |
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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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dump_out->writeFinal(); |
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delete dump_out; |
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delete e_out; |
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} |
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void Integrator::integrateStep( int calcPot, int calcStress ){ |
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// Position full step, and velocity half step |
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//preMove(); |
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moveA(); |
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if( nConstrained ) constrainA(); |
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// calc forces |
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myFF->doForces(calcPot,calcStress); |
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// finish the velocity half step |
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moveB(); |
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if( nConstrained ) constrainB(); |
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} |
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void Integrator::moveA( void ){ |
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int i,j,k; |
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int atomIndex, aMatIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
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// position whole step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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pos[j] += dt * vel[j]; |
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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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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
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ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
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ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * 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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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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} |
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} |
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} |
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void Integrator::moveB( void ){ |
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int i,j,k; |
| 348 |
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int atomIndex; |
| 349 |
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DirectionalAtom* dAtom; |
| 350 |
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double Tb[3]; |
| 351 |
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double ji[3]; |
| 352 |
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| 353 |
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for( i=0; i<nAtoms; i++ ){ |
| 354 |
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atomIndex = i * 3; |
| 355 |
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| 356 |
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// velocity half step |
| 357 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 358 |
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vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
| 359 |
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| 360 |
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if( atoms[i]->isDirectional() ){ |
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| 362 |
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dAtom = (DirectionalAtom *)atoms[i]; |
| 363 |
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| 364 |
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// get and convert the torque to body frame |
| 365 |
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| 366 |
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Tb[0] = dAtom->getTx(); |
| 367 |
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Tb[1] = dAtom->getTy(); |
| 368 |
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Tb[2] = dAtom->getTz(); |
| 369 |
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| 370 |
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dAtom->lab2Body( Tb ); |
| 371 |
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| 372 |
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// get the angular momentum, and complete the angular momentum |
| 373 |
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// half step |
| 374 |
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| 375 |
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ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
| 376 |
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ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
| 377 |
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ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
| 378 |
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| 379 |
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jx2 = ji[0] * ji[0]; |
| 380 |
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jy2 = ji[1] * ji[1]; |
| 381 |
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jz2 = ji[2] * ji[2]; |
| 382 |
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| 383 |
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dAtom->setJx( ji[0] ); |
| 384 |
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dAtom->setJy( ji[1] ); |
| 385 |
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dAtom->setJz( ji[2] ); |
| 386 |
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} |
| 387 |
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} |
| 388 |
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| 389 |
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} |
| 390 |
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| 391 |
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void Integrator::preMove( void ){ |
| 392 |
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int i; |
| 393 |
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| 394 |
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if( nConstrained ){ |
| 395 |
|
|
if( oldAtoms != nAtoms ){ |
| 396 |
|
|
|
| 397 |
|
|
// save oldAtoms to check for lode balanceing later on. |
| 398 |
|
|
|
| 399 |
|
|
oldAtoms = nAtoms; |
| 400 |
|
|
|
| 401 |
|
|
delete[] moving; |
| 402 |
|
|
delete[] moved; |
| 403 |
|
|
delete[] oldPos; |
| 404 |
|
|
|
| 405 |
|
|
moving = new int[nAtoms]; |
| 406 |
|
|
moved = new int[nAtoms]; |
| 407 |
|
|
|
| 408 |
|
|
oldPos = new double[nAtoms*3]; |
| 409 |
|
|
} |
| 410 |
|
|
|
| 411 |
|
|
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
| 412 |
|
|
} |
| 413 |
|
|
} |
| 414 |
|
|
|
| 415 |
|
|
void Integrator::constrainA(){ |
| 416 |
|
|
|
| 417 |
|
|
int i,j,k; |
| 418 |
|
|
int done; |
| 419 |
|
|
double pxab, pyab, pzab; |
| 420 |
|
|
double rxab, ryab, rzab; |
| 421 |
|
|
int a, b; |
| 422 |
|
|
double rma, rmb; |
| 423 |
|
|
double dx, dy, dz; |
| 424 |
|
|
double rabsq, pabsq, rpabsq; |
| 425 |
|
|
double diffsq; |
| 426 |
|
|
double gab; |
| 427 |
|
|
int iteration; |
| 428 |
|
|
|
| 429 |
|
|
|
| 430 |
|
|
|
| 431 |
|
|
for( i=0; i<nAtoms; i++){ |
| 432 |
|
|
|
| 433 |
|
|
moving[i] = 0; |
| 434 |
|
|
moved[i] = 1; |
| 435 |
|
|
} |
| 436 |
|
|
|
| 437 |
|
|
|
| 438 |
|
|
iteration = 0; |
| 439 |
|
|
done = 0; |
| 440 |
|
|
while( !done && (iteration < maxIteration )){ |
| 441 |
|
|
|
| 442 |
|
|
done = 1; |
| 443 |
|
|
for(i=0; i<nConstrained; i++){ |
| 444 |
|
|
|
| 445 |
|
|
a = constrainedA[i]; |
| 446 |
|
|
b = constrainedB[i]; |
| 447 |
|
|
|
| 448 |
|
|
if( moved[a] || moved[b] ){ |
| 449 |
|
|
|
| 450 |
|
|
pxab = pos[3*a+0] - pos[3*b+0]; |
| 451 |
|
|
pyab = pos[3*a+1] - pos[3*b+1]; |
| 452 |
|
|
pzab = pos[3*a+2] - pos[3*b+2]; |
| 453 |
|
|
|
| 454 |
|
|
//periodic boundary condition |
| 455 |
|
|
pxab = pxab - info->box_x * copysign(1, pxab) |
| 456 |
|
|
* int(pxab / info->box_x + 0.5); |
| 457 |
|
|
pyab = pyab - info->box_y * copysign(1, pyab) |
| 458 |
|
|
* int(pyab / info->box_y + 0.5); |
| 459 |
|
|
pzab = pzab - info->box_z * copysign(1, pzab) |
| 460 |
|
|
* int(pzab / info->box_z + 0.5); |
| 461 |
|
|
|
| 462 |
|
|
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
| 463 |
|
|
rabsq = constraintedDsqr[i]; |
| 464 |
|
|
diffsq = pabsq - rabsq; |
| 465 |
|
|
|
| 466 |
|
|
// the original rattle code from alan tidesley |
| 467 |
|
|
if (fabs(diffsq) > tol*rabsq*2) { |
| 468 |
|
|
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
| 469 |
|
|
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
| 470 |
|
|
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
| 471 |
|
|
|
| 472 |
|
|
rxab = rxab - info->box_x * copysign(1, rxab) |
| 473 |
|
|
* int(rxab / info->box_x + 0.5); |
| 474 |
|
|
ryab = ryab - info->box_y * copysign(1, ryab) |
| 475 |
|
|
* int(ryab / info->box_y + 0.5); |
| 476 |
|
|
rzab = rzab - info->box_z * copysign(1, rzab) |
| 477 |
|
|
* int(rzab / info->box_z + 0.5); |
| 478 |
|
|
|
| 479 |
|
|
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
| 480 |
|
|
rpabsq = rpab * rpab; |
| 481 |
|
|
|
| 482 |
|
|
|
| 483 |
|
|
if (rpabsq < (rabsq * -diffsq)){ |
| 484 |
|
|
#ifdef IS_MPI |
| 485 |
|
|
a = atoms[a]->getGlobalIndex(); |
| 486 |
|
|
b = atoms[b]->getGlobalIndex(); |
| 487 |
|
|
#endif //is_mpi |
| 488 |
|
|
sprintf( painCave.errMsg, |
| 489 |
|
|
"Constraint failure in constrainA at atom %d and %d\n.", |
| 490 |
|
|
a, b ); |
| 491 |
|
|
painCave.isFatal = 1; |
| 492 |
|
|
simError(); |
| 493 |
|
|
} |
| 494 |
|
|
|
| 495 |
|
|
rma = 1.0 / atoms[a]->getMass(); |
| 496 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
| 497 |
|
|
|
| 498 |
|
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
| 499 |
|
|
dx = rxab * gab; |
| 500 |
|
|
dy = ryab * gab; |
| 501 |
|
|
dz = rzab * gab; |
| 502 |
|
|
|
| 503 |
|
|
pos[3*a+0] += rma * dx; |
| 504 |
|
|
pos[3*a+1] += rma * dy; |
| 505 |
|
|
pos[3*a+2] += rma * dz; |
| 506 |
|
|
|
| 507 |
|
|
pos[3*b+0] -= rmb * dx; |
| 508 |
|
|
pos[3*b+1] -= rmb * dy; |
| 509 |
|
|
pos[3*b+2] -= rmb * dz; |
| 510 |
|
|
|
| 511 |
|
|
dx = dx / dt; |
| 512 |
|
|
dy = dy / dt; |
| 513 |
|
|
dz = dz / dt; |
| 514 |
|
|
|
| 515 |
|
|
vel[3*a+0] += rma * dx; |
| 516 |
|
|
vel[3*a+1] += rma * dy; |
| 517 |
|
|
vel[3*a+2] += rma * dz; |
| 518 |
|
|
|
| 519 |
|
|
vel[3*b+0] -= rmb * dx; |
| 520 |
|
|
vel[3*b+1] -= rmb * dy; |
| 521 |
|
|
vel[3*b+2] -= rmb * dz; |
| 522 |
|
|
|
| 523 |
|
|
moving[a] = 1; |
| 524 |
|
|
moving[b] = 1; |
| 525 |
|
|
done = 0; |
| 526 |
|
|
} |
| 527 |
|
|
} |
| 528 |
|
|
} |
| 529 |
|
|
|
| 530 |
|
|
for(i=0; i<nAtoms; i++){ |
| 531 |
|
|
|
| 532 |
|
|
moved[i] = moving[i]; |
| 533 |
|
|
moving[i] = 0; |
| 534 |
|
|
} |
| 535 |
|
|
|
| 536 |
|
|
iteration++; |
| 537 |
|
|
} |
| 538 |
|
|
|
| 539 |
|
|
if( !done ){ |
| 540 |
|
|
|
| 541 |
|
|
sprintf( painCae.errMsg, |
| 542 |
|
|
"Constraint failure in constrainA, too many iterations: %d\n", |
| 543 |
|
|
iterations ); |
| 544 |
|
|
painCave.isFatal = 1; |
| 545 |
|
|
simError(); |
| 546 |
|
|
} |
| 547 |
|
|
|
| 548 |
|
|
} |
| 549 |
|
|
|
| 550 |
|
|
void Integrator::constrainB( void ){ |
| 551 |
|
|
|
| 552 |
|
|
int i,j,k; |
| 553 |
|
|
int done; |
| 554 |
|
|
double vxab, vyab, vzab; |
| 555 |
|
|
double rxab, ryab, rzab; |
| 556 |
|
|
int a, b; |
| 557 |
|
|
double rma, rmb; |
| 558 |
|
|
double dx, dy, dz; |
| 559 |
|
|
double rabsq, pabsq, rvab; |
| 560 |
|
|
double diffsq; |
| 561 |
|
|
double gab; |
| 562 |
|
|
int iteration; |
| 563 |
|
|
|
| 564 |
|
|
for(i=0; i<nAtom; i++){ |
| 565 |
|
|
moving[i] = 0; |
| 566 |
|
|
moved[i] = 1; |
| 567 |
|
|
} |
| 568 |
|
|
|
| 569 |
|
|
done = 0; |
| 570 |
|
|
while( !done && (iteration < maxIteration ) ){ |
| 571 |
|
|
|
| 572 |
|
|
for(i=0; i<nConstrained; i++){ |
| 573 |
|
|
|
| 574 |
|
|
a = constrainedA[i]; |
| 575 |
|
|
b = constrainedB[i]; |
| 576 |
|
|
|
| 577 |
|
|
if( moved[a] || moved[b] ){ |
| 578 |
|
|
|
| 579 |
|
|
vxab = vel[3*a+0] - vel[3*b+0]; |
| 580 |
|
|
vyab = vel[3*a+1] - vel[3*b+1]; |
| 581 |
|
|
vzab = vel[3*a+2] - vel[3*b+2]; |
| 582 |
|
|
|
| 583 |
|
|
rxab = pos[3*a+0] - pos[3*b+0];q |
| 584 |
|
|
ryab = pos[3*a+1] - pos[3*b+1]; |
| 585 |
|
|
rzab = pos[3*a+2] - pos[3*b+2]; |
| 586 |
|
|
|
| 587 |
|
|
rxab = rxab - info->box_x * copysign(1, rxab) |
| 588 |
|
|
* int(rxab / info->box_x + 0.5); |
| 589 |
|
|
ryab = ryab - info->box_y * copysign(1, ryab) |
| 590 |
|
|
* int(ryab / info->box_y + 0.5); |
| 591 |
|
|
rzab = rzab - info->box_z * copysign(1, rzab) |
| 592 |
|
|
* int(rzab / info->box_z + 0.5); |
| 593 |
|
|
|
| 594 |
|
|
rma = 1.0 / atoms[a]->getMass(); |
| 595 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
| 596 |
|
|
|
| 597 |
|
|
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
| 598 |
|
|
|
| 599 |
|
|
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
| 600 |
|
|
|
| 601 |
|
|
if (fabs(gab) > tol) { |
| 602 |
|
|
|
| 603 |
|
|
dx = rxab * gab; |
| 604 |
|
|
dy = ryab * gab; |
| 605 |
|
|
dz = rzab * gab; |
| 606 |
|
|
|
| 607 |
|
|
vel[3*a+0] += rma * dx; |
| 608 |
|
|
vel[3*a+1] += rma * dy; |
| 609 |
|
|
vel[3*a+2] += rma * dz; |
| 610 |
|
|
|
| 611 |
|
|
vel[3*b+0] -= rmb * dx; |
| 612 |
|
|
vel[3*b+1] -= rmb * dy; |
| 613 |
|
|
vel[3*b+2] -= rmb * dz; |
| 614 |
|
|
|
| 615 |
|
|
moving[a] = 1; |
| 616 |
|
|
moving[b] = 1; |
| 617 |
|
|
done = 0; |
| 618 |
|
|
} |
| 619 |
|
|
} |
| 620 |
|
|
} |
| 621 |
|
|
|
| 622 |
|
|
for(i=0; i<nAtoms; i++){ |
| 623 |
|
|
moved[i] = moving[i]; |
| 624 |
|
|
moving[i] = 0; |
| 625 |
|
|
} |
| 626 |
|
|
|
| 627 |
|
|
iteration++; |
| 628 |
|
|
} |
| 629 |
|
|
|
| 630 |
|
|
if( !done ){ |
| 631 |
|
|
|
| 632 |
|
|
|
| 633 |
|
|
sprintf( painCae.errMsg, |
| 634 |
|
|
"Constraint failure in constrainB, too many iterations: %d\n", |
| 635 |
|
|
iterations ); |
| 636 |
|
|
painCave.isFatal = 1; |
| 637 |
|
|
simError(); |
| 638 |
|
|
} |
| 639 |
|
|
|
| 640 |
|
|
} |
| 641 |
|
|
|
| 642 |
|
|
|
| 643 |
|
|
|
| 644 |
|
|
|
| 645 |
|
|
|
| 646 |
|
|
|
| 647 |
|
|
|
| 648 |
|
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
| 649 |
|
|
double A[3][3] ){ |
| 650 |
|
|
|
| 651 |
|
|
int i,j,k; |
| 652 |
|
|
double sinAngle; |
| 653 |
|
|
double cosAngle; |
| 654 |
|
|
double angleSqr; |
| 655 |
|
|
double angleSqrOver4; |
| 656 |
|
|
double top, bottom; |
| 657 |
|
|
double rot[3][3]; |
| 658 |
|
|
double tempA[3][3]; |
| 659 |
|
|
double tempJ[3]; |
| 660 |
|
|
|
| 661 |
|
|
// initialize the tempA |
| 662 |
|
|
|
| 663 |
|
|
for(i=0; i<3; i++){ |
| 664 |
|
|
for(j=0; j<3; j++){ |
| 665 |
|
|
tempA[j][i] = A[i][j]; |
| 666 |
|
|
} |
| 667 |
|
|
} |
| 668 |
|
|
|
| 669 |
|
|
// initialize the tempJ |
| 670 |
|
|
|
| 671 |
|
|
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
| 672 |
|
|
|
| 673 |
|
|
// initalize rot as a unit matrix |
| 674 |
|
|
|
| 675 |
|
|
rot[0][0] = 1.0; |
| 676 |
|
|
rot[0][1] = 0.0; |
| 677 |
|
|
rot[0][2] = 0.0; |
| 678 |
|
|
|
| 679 |
|
|
rot[1][0] = 0.0; |
| 680 |
|
|
rot[1][1] = 1.0; |
| 681 |
|
|
rot[1][2] = 0.0; |
| 682 |
|
|
|
| 683 |
|
|
rot[2][0] = 0.0; |
| 684 |
|
|
rot[2][1] = 0.0; |
| 685 |
|
|
rot[2][2] = 1.0; |
| 686 |
|
|
|
| 687 |
|
|
// use a small angle aproximation for sin and cosine |
| 688 |
|
|
|
| 689 |
|
|
angleSqr = angle * angle; |
| 690 |
|
|
angleSqrOver4 = angleSqr / 4.0; |
| 691 |
|
|
top = 1.0 - angleSqrOver4; |
| 692 |
|
|
bottom = 1.0 + angleSqrOver4; |
| 693 |
|
|
|
| 694 |
|
|
cosAngle = top / bottom; |
| 695 |
|
|
sinAngle = angle / bottom; |
| 696 |
|
|
|
| 697 |
|
|
rot[axes1][axes1] = cosAngle; |
| 698 |
|
|
rot[axes2][axes2] = cosAngle; |
| 699 |
|
|
|
| 700 |
|
|
rot[axes1][axes2] = sinAngle; |
| 701 |
|
|
rot[axes2][axes1] = -sinAngle; |
| 702 |
|
|
|
| 703 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
| 704 |
|
|
|
| 705 |
|
|
for(i=0; i<3; i++){ |
| 706 |
|
|
ji[i] = 0.0; |
| 707 |
|
|
for(k=0; k<3; k++){ |
| 708 |
|
|
ji[i] += rot[i][k] * tempJ[k]; |
| 709 |
|
|
} |
| 710 |
|
|
} |
| 711 |
|
|
|
| 712 |
|
|
// rotate the Rotation matrix acording to: |
| 713 |
|
|
// A[][] = A[][] * transpose(rot[][]) |
| 714 |
|
|
|
| 715 |
|
|
|
| 716 |
|
|
// NOte for as yet unknown reason, we are setting the performing the |
| 717 |
|
|
// calculation as: |
| 718 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
| 719 |
|
|
|
| 720 |
|
|
for(i=0; i<3; i++){ |
| 721 |
|
|
for(j=0; j<3; j++){ |
| 722 |
|
|
A[j][i] = 0.0; |
| 723 |
|
|
for(k=0; k<3; k++){ |
| 724 |
|
|
A[j][i] += tempA[i][k] * rot[j][k]; |
| 725 |
|
|
} |
| 726 |
|
|
} |
| 727 |
|
|
} |
| 728 |
|
|
} |
