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#include <iostream> |
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#include <cstdlib> |
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|
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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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|
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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|
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Symplectic::Symplectic( SimInfo* theInfo, ForceFields* the_ff ){ |
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|
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info = theInfo; |
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myFF = the_ff; |
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isFirst = 1; |
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|
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molecules = info->molecules; |
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nMols = info->n_mol; |
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|
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// give a little love back to the SimInfo object |
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|
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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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|
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// check for constraints |
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|
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constrainedI = NULL; |
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constrainedJ = NULL; |
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constrainedDsqr = NULL; |
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nConstrained = 0; |
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|
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checkConstraints(); |
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} |
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|
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Symplectic::~Symplectic() { |
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|
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if( nConstrained ){ |
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delete[] constrainedI; |
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delete[] constrainedJ; |
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delete[] constrainedDsqr; |
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} |
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|
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} |
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|
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void Symplectic::checkConstraints( void ){ |
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|
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|
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isConstrained = 0; |
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|
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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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|
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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|
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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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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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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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|
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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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theArray = (SRI**) molecules[i].getMyBends(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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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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|
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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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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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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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|
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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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|
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if(nConstrained > 0){ |
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|
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isConstrained = 1; |
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|
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if(constrainedI != NULL ) delete[] constrainedI; |
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if(constrainedJ != NULL ) delete[] constrainedJ; |
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if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
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|
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constrainedI = new int[nConstrained]; |
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constrainedJ = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
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|
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for( int i = 0; i < nConstrained; i++){ |
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constrainedI[i] = temp_con[i].get_a(); |
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constrainedJ[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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} |
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|
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delete[] temp_con; |
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} |
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|
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|
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void Symplectic::integrate( void ){ |
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|
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int i, j; // loop counters |
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int nAtoms = info->n_atoms; // the number of atoms |
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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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|
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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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|
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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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|
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int time; |
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|
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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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|
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int n_loops = (int)( runTime / dt ); |
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int sample_n = (int)( sampleTime / dt ); |
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int status_n = (int)( statusTime / dt ); |
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int vel_n = (int)( thermalTime / dt ); |
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|
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int calcPot, calcStress; |
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int isError; |
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|
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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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|
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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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|
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// initialize the forces before the first step |
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|
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myFF->doForces(1,1); |
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|
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if( info->setTemp ){ |
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|
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tStats->velocitize(); |
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} |
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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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|
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for( tl=0; tl<nLoops; tl++){ |
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integrateStep( calcPot, calcStress ); |
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|
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time = tl + 1; |
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|
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if( info->setTemp ){ |
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if( !(time % vel_n) ) tStats->velocitize(); |
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} |
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if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
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if( !((time+1) % status_n) ) { |
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calcPot = 1; |
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calcStress = 1; |
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} |
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if( !(time % status_n) ){ |
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e_out->writeStat( time * dt ); |
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calcPot = 0; |
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if (!strcasecmp(info->ensemble, "NPT")) calcStress = 1; |
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else calcStress = 0; |
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} |
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|
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|
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} |
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|
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dump_out->writeFinal(); |
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|
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delete dump_out; |
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delete e_out; |
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} |
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|
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|
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void Symplectic::moveA( void ){ |
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|
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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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|
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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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|
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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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|
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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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|
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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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// get and convert the torque to body frame |
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|
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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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|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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|
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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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|
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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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// 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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|
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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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|
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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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|
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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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|
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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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} |
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|
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|
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void Integrator::moveB( void ){ |
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int i,j,k; |
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int atomIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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|
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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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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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// get and convert the torque to body frame |
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|
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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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|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and complete the angular momentum |
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// half step |
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|
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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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|
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jx2 = ji[0] * ji[0]; |
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jy2 = ji[1] * ji[1]; |
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jz2 = ji[2] * ji[2]; |
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|
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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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} |
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|
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|
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void Integrator::constrainA(){ |
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|
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|
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|
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|
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} |
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|
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|
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void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
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double A[3][3] ){ |
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|
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int i,j,k; |
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double sinAngle; |
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double cosAngle; |
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double angleSqr; |
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double angleSqrOver4; |
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double top, bottom; |
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double rot[3][3]; |
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double tempA[3][3]; |
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double tempJ[3]; |
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|
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// initialize the tempA |
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|
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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tempA[j][i] = A[i][j]; |
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} |
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} |
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|
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// initialize the tempJ |
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|
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for( i=0; i<3; i++) tempJ[i] = ji[i]; |
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|
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// initalize rot as a unit matrix |
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|
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rot[0][0] = 1.0; |
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rot[0][1] = 0.0; |
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rot[0][2] = 0.0; |
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|
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rot[1][0] = 0.0; |
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rot[1][1] = 1.0; |
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rot[1][2] = 0.0; |
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|
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rot[2][0] = 0.0; |
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rot[2][1] = 0.0; |
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rot[2][2] = 1.0; |
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|
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// use a small angle aproximation for sin and cosine |
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|
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angleSqr = angle * angle; |
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angleSqrOver4 = angleSqr / 4.0; |
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top = 1.0 - angleSqrOver4; |
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bottom = 1.0 + angleSqrOver4; |
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|
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cosAngle = top / bottom; |
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sinAngle = angle / bottom; |
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|
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rot[axes1][axes1] = cosAngle; |
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rot[axes2][axes2] = cosAngle; |
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|
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rot[axes1][axes2] = sinAngle; |
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rot[axes2][axes1] = -sinAngle; |
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|
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// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
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|
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for(i=0; i<3; i++){ |
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ji[i] = 0.0; |
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for(k=0; k<3; k++){ |
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ji[i] += rot[i][k] * tempJ[k]; |
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} |
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} |
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|
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// rotate the Rotation matrix acording to: |
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// A[][] = A[][] * transpose(rot[][]) |
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|
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|
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// NOte for as yet unknown reason, we are setting the performing the |
| 428 |
// calculation as: |
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// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
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|
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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A[j][i] = 0.0; |
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for(k=0; k<3; k++){ |
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A[j][i] += tempA[i][k] * rot[j][k]; |
| 436 |
} |
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} |
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} |
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} |
