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#include <iostream> |
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#include <cstdlib> |
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#include <cmath> |
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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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oldPos = 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[] oldPos; |
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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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cerr << "constraint " << constrainedA[i] << " <-> " << constrainedB[i] |
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<< " => " << constrainedDsqr[i] << "\n"; |
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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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oldPos = 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 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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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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// 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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dumpOut->writeDump( 0.0 ); |
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statOut->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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readyCheck(); |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, |
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"The integrator is ready to go." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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pos = Atom::getPosArray(); |
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vel = Atom::getVelArray(); |
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frc = Atom::getFrcArray(); |
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trq = Atom::getTrqArray(); |
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Amat = Atom::getAmatArray(); |
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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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dumpOut->writeDump( currTime ); |
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currSample += sampleTime; |
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} |
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if( currTime >= currStatus ){ |
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statOut->writeStat( currTime ); |
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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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#ifdef IS_MPI |
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strcpy( checkPointMsg, |
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"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(); |
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delete dumpOut; |
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delete statOut; |
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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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double angle; |
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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; |
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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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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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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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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 complete the angular momentum |
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// 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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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::preMove( void ){ |
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int i; |
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if( nConstrained ){ |
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mmeineke |
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|
408 |
mmeineke |
558 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
409 |
|
|
} |
410 |
|
|
} |
411 |
|
|
|
412 |
|
|
void Integrator::constrainA(){ |
413 |
|
|
|
414 |
|
|
int i,j,k; |
415 |
|
|
int done; |
416 |
|
|
double pxab, pyab, pzab; |
417 |
|
|
double rxab, ryab, rzab; |
418 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
419 |
mmeineke |
558 |
double rma, rmb; |
420 |
|
|
double dx, dy, dz; |
421 |
mmeineke |
561 |
double rpab; |
422 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
423 |
|
|
double diffsq; |
424 |
|
|
double gab; |
425 |
|
|
int iteration; |
426 |
|
|
|
427 |
|
|
|
428 |
|
|
|
429 |
|
|
for( i=0; i<nAtoms; i++){ |
430 |
|
|
|
431 |
|
|
moving[i] = 0; |
432 |
|
|
moved[i] = 1; |
433 |
|
|
} |
434 |
|
|
|
435 |
|
|
|
436 |
|
|
iteration = 0; |
437 |
|
|
done = 0; |
438 |
|
|
while( !done && (iteration < maxIteration )){ |
439 |
|
|
|
440 |
|
|
done = 1; |
441 |
|
|
for(i=0; i<nConstrained; i++){ |
442 |
|
|
|
443 |
|
|
a = constrainedA[i]; |
444 |
|
|
b = constrainedB[i]; |
445 |
mmeineke |
563 |
|
446 |
|
|
ax = (a*3) + 0; |
447 |
|
|
ay = (a*3) + 1; |
448 |
|
|
az = (a*3) + 2; |
449 |
|
|
|
450 |
|
|
bx = (b*3) + 0; |
451 |
|
|
by = (b*3) + 1; |
452 |
|
|
bz = (b*3) + 2; |
453 |
|
|
|
454 |
|
|
|
455 |
mmeineke |
558 |
if( moved[a] || moved[b] ){ |
456 |
|
|
|
457 |
mmeineke |
563 |
pxab = pos[ax] - pos[bx]; |
458 |
|
|
pyab = pos[ay] - pos[by]; |
459 |
|
|
pzab = pos[az] - pos[bz]; |
460 |
mmeineke |
558 |
|
461 |
|
|
//periodic boundary condition |
462 |
|
|
pxab = pxab - info->box_x * copysign(1, pxab) |
463 |
mmeineke |
563 |
* (int)( fabs(pxab / info->box_x) + 0.5); |
464 |
mmeineke |
558 |
pyab = pyab - info->box_y * copysign(1, pyab) |
465 |
mmeineke |
563 |
* (int)( fabs(pyab / info->box_y) + 0.5); |
466 |
mmeineke |
558 |
pzab = pzab - info->box_z * copysign(1, pzab) |
467 |
mmeineke |
563 |
* (int)( fabs(pzab / info->box_z) + 0.5); |
468 |
mmeineke |
558 |
|
469 |
|
|
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
470 |
mmeineke |
561 |
rabsq = constrainedDsqr[i]; |
471 |
mmeineke |
558 |
diffsq = pabsq - rabsq; |
472 |
|
|
|
473 |
|
|
// the original rattle code from alan tidesley |
474 |
mmeineke |
563 |
if (fabs(diffsq) > (tol*rabsq*2)) { |
475 |
|
|
rxab = oldPos[ax] - oldPos[bx]; |
476 |
|
|
ryab = oldPos[ay] - oldPos[by]; |
477 |
|
|
rzab = oldPos[az] - oldPos[bz]; |
478 |
mmeineke |
558 |
|
479 |
|
|
rxab = rxab - info->box_x * copysign(1, rxab) |
480 |
mmeineke |
563 |
* (int)( fabs(rxab / info->box_x) + 0.5); |
481 |
mmeineke |
558 |
ryab = ryab - info->box_y * copysign(1, ryab) |
482 |
mmeineke |
563 |
* (int)( fabs(ryab / info->box_y) + 0.5); |
483 |
mmeineke |
558 |
rzab = rzab - info->box_z * copysign(1, rzab) |
484 |
mmeineke |
563 |
* (int)( fabs(rzab / info->box_z) + 0.5); |
485 |
mmeineke |
558 |
|
486 |
|
|
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
487 |
|
|
rpabsq = rpab * rpab; |
488 |
|
|
|
489 |
|
|
|
490 |
|
|
if (rpabsq < (rabsq * -diffsq)){ |
491 |
mmeineke |
563 |
|
492 |
|
|
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
|
|
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
|
|
|
495 |
mmeineke |
558 |
#ifdef IS_MPI |
496 |
|
|
a = atoms[a]->getGlobalIndex(); |
497 |
|
|
b = atoms[b]->getGlobalIndex(); |
498 |
|
|
#endif //is_mpi |
499 |
|
|
sprintf( painCave.errMsg, |
500 |
mmeineke |
563 |
"Constraint failure in constrainA at atom %d and %d.\n", |
501 |
mmeineke |
558 |
a, b ); |
502 |
|
|
painCave.isFatal = 1; |
503 |
|
|
simError(); |
504 |
|
|
} |
505 |
|
|
|
506 |
|
|
rma = 1.0 / atoms[a]->getMass(); |
507 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
508 |
|
|
|
509 |
|
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
510 |
|
|
dx = rxab * gab; |
511 |
|
|
dy = ryab * gab; |
512 |
|
|
dz = rzab * gab; |
513 |
|
|
|
514 |
mmeineke |
563 |
pos[ax] += rma * dx; |
515 |
|
|
pos[ay] += rma * dy; |
516 |
|
|
pos[az] += rma * dz; |
517 |
mmeineke |
558 |
|
518 |
mmeineke |
563 |
pos[bx] -= rmb * dx; |
519 |
|
|
pos[by] -= rmb * dy; |
520 |
|
|
pos[bz] -= rmb * dz; |
521 |
mmeineke |
558 |
|
522 |
|
|
dx = dx / dt; |
523 |
|
|
dy = dy / dt; |
524 |
|
|
dz = dz / dt; |
525 |
|
|
|
526 |
mmeineke |
563 |
vel[ax] += rma * dx; |
527 |
|
|
vel[ay] += rma * dy; |
528 |
|
|
vel[az] += rma * dz; |
529 |
mmeineke |
558 |
|
530 |
mmeineke |
563 |
vel[bx] -= rmb * dx; |
531 |
|
|
vel[by] -= rmb * dy; |
532 |
|
|
vel[bz] -= rmb * dz; |
533 |
mmeineke |
558 |
|
534 |
|
|
moving[a] = 1; |
535 |
|
|
moving[b] = 1; |
536 |
|
|
done = 0; |
537 |
|
|
} |
538 |
|
|
} |
539 |
|
|
} |
540 |
|
|
|
541 |
|
|
for(i=0; i<nAtoms; i++){ |
542 |
|
|
|
543 |
|
|
moved[i] = moving[i]; |
544 |
|
|
moving[i] = 0; |
545 |
|
|
} |
546 |
|
|
|
547 |
|
|
iteration++; |
548 |
mmeineke |
563 |
cerr << "iterainA = " << iteration << "\n"; |
549 |
mmeineke |
558 |
} |
550 |
|
|
|
551 |
|
|
if( !done ){ |
552 |
|
|
|
553 |
mmeineke |
561 |
sprintf( painCave.errMsg, |
554 |
mmeineke |
558 |
"Constraint failure in constrainA, too many iterations: %d\n", |
555 |
mmeineke |
561 |
iteration ); |
556 |
mmeineke |
558 |
painCave.isFatal = 1; |
557 |
|
|
simError(); |
558 |
|
|
} |
559 |
|
|
|
560 |
|
|
} |
561 |
|
|
|
562 |
|
|
void Integrator::constrainB( void ){ |
563 |
|
|
|
564 |
|
|
int i,j,k; |
565 |
|
|
int done; |
566 |
|
|
double vxab, vyab, vzab; |
567 |
|
|
double rxab, ryab, rzab; |
568 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
569 |
mmeineke |
558 |
double rma, rmb; |
570 |
|
|
double dx, dy, dz; |
571 |
|
|
double rabsq, pabsq, rvab; |
572 |
|
|
double diffsq; |
573 |
|
|
double gab; |
574 |
|
|
int iteration; |
575 |
|
|
|
576 |
mmeineke |
561 |
for(i=0; i<nAtoms; i++){ |
577 |
mmeineke |
558 |
moving[i] = 0; |
578 |
|
|
moved[i] = 1; |
579 |
|
|
} |
580 |
|
|
|
581 |
|
|
done = 0; |
582 |
mmeineke |
561 |
iteration = 0; |
583 |
mmeineke |
558 |
while( !done && (iteration < maxIteration ) ){ |
584 |
|
|
|
585 |
|
|
for(i=0; i<nConstrained; i++){ |
586 |
|
|
|
587 |
|
|
a = constrainedA[i]; |
588 |
|
|
b = constrainedB[i]; |
589 |
|
|
|
590 |
mmeineke |
563 |
ax = 3*a +0; |
591 |
|
|
ay = 3*a +1; |
592 |
|
|
az = 3*a +2; |
593 |
|
|
|
594 |
|
|
bx = 3*b +0; |
595 |
|
|
by = 3*b +1; |
596 |
|
|
bz = 3*b +2; |
597 |
|
|
|
598 |
mmeineke |
558 |
if( moved[a] || moved[b] ){ |
599 |
|
|
|
600 |
mmeineke |
563 |
vxab = vel[ax] - vel[bx]; |
601 |
|
|
vyab = vel[ay] - vel[by]; |
602 |
|
|
vzab = vel[az] - vel[bz]; |
603 |
mmeineke |
558 |
|
604 |
mmeineke |
563 |
rxab = pos[ax] - pos[bx]; |
605 |
|
|
ryab = pos[ay] - pos[by]; |
606 |
|
|
rzab = pos[az] - pos[bz]; |
607 |
mmeineke |
558 |
|
608 |
|
|
rxab = rxab - info->box_x * copysign(1, rxab) |
609 |
mmeineke |
563 |
* (int)( fabs(rxab / info->box_x) + 0.5); |
610 |
mmeineke |
558 |
ryab = ryab - info->box_y * copysign(1, ryab) |
611 |
mmeineke |
563 |
* (int)( fabs(ryab / info->box_y) + 0.5); |
612 |
mmeineke |
558 |
rzab = rzab - info->box_z * copysign(1, rzab) |
613 |
mmeineke |
563 |
* (int)( fabs(rzab / info->box_z) + 0.5); |
614 |
mmeineke |
558 |
|
615 |
|
|
rma = 1.0 / atoms[a]->getMass(); |
616 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
617 |
|
|
|
618 |
|
|
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
619 |
|
|
|
620 |
mmeineke |
561 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
621 |
mmeineke |
558 |
|
622 |
|
|
if (fabs(gab) > tol) { |
623 |
|
|
|
624 |
|
|
dx = rxab * gab; |
625 |
|
|
dy = ryab * gab; |
626 |
|
|
dz = rzab * gab; |
627 |
|
|
|
628 |
mmeineke |
563 |
vel[ax] += rma * dx; |
629 |
|
|
vel[ay] += rma * dy; |
630 |
|
|
vel[az] += rma * dz; |
631 |
mmeineke |
558 |
|
632 |
mmeineke |
563 |
vel[bx] -= rmb * dx; |
633 |
|
|
vel[by] -= rmb * dy; |
634 |
|
|
vel[bz] -= rmb * dz; |
635 |
mmeineke |
558 |
|
636 |
|
|
moving[a] = 1; |
637 |
|
|
moving[b] = 1; |
638 |
|
|
done = 0; |
639 |
|
|
} |
640 |
|
|
} |
641 |
|
|
} |
642 |
|
|
|
643 |
|
|
for(i=0; i<nAtoms; i++){ |
644 |
|
|
moved[i] = moving[i]; |
645 |
|
|
moving[i] = 0; |
646 |
|
|
} |
647 |
|
|
|
648 |
|
|
iteration++; |
649 |
|
|
} |
650 |
|
|
|
651 |
|
|
if( !done ){ |
652 |
|
|
|
653 |
|
|
|
654 |
mmeineke |
561 |
sprintf( painCave.errMsg, |
655 |
mmeineke |
558 |
"Constraint failure in constrainB, too many iterations: %d\n", |
656 |
mmeineke |
561 |
iteration ); |
657 |
mmeineke |
558 |
painCave.isFatal = 1; |
658 |
|
|
simError(); |
659 |
|
|
} |
660 |
|
|
|
661 |
|
|
} |
662 |
|
|
|
663 |
|
|
|
664 |
|
|
|
665 |
|
|
|
666 |
|
|
|
667 |
|
|
|
668 |
|
|
|
669 |
|
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
670 |
mmeineke |
561 |
double A[9] ){ |
671 |
mmeineke |
558 |
|
672 |
|
|
int i,j,k; |
673 |
|
|
double sinAngle; |
674 |
|
|
double cosAngle; |
675 |
|
|
double angleSqr; |
676 |
|
|
double angleSqrOver4; |
677 |
|
|
double top, bottom; |
678 |
|
|
double rot[3][3]; |
679 |
|
|
double tempA[3][3]; |
680 |
|
|
double tempJ[3]; |
681 |
|
|
|
682 |
|
|
// initialize the tempA |
683 |
|
|
|
684 |
|
|
for(i=0; i<3; i++){ |
685 |
|
|
for(j=0; j<3; j++){ |
686 |
mmeineke |
561 |
tempA[j][i] = A[3*i + j]; |
687 |
mmeineke |
558 |
} |
688 |
|
|
} |
689 |
|
|
|
690 |
|
|
// initialize the tempJ |
691 |
|
|
|
692 |
|
|
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
693 |
|
|
|
694 |
|
|
// initalize rot as a unit matrix |
695 |
|
|
|
696 |
|
|
rot[0][0] = 1.0; |
697 |
|
|
rot[0][1] = 0.0; |
698 |
|
|
rot[0][2] = 0.0; |
699 |
|
|
|
700 |
|
|
rot[1][0] = 0.0; |
701 |
|
|
rot[1][1] = 1.0; |
702 |
|
|
rot[1][2] = 0.0; |
703 |
|
|
|
704 |
|
|
rot[2][0] = 0.0; |
705 |
|
|
rot[2][1] = 0.0; |
706 |
|
|
rot[2][2] = 1.0; |
707 |
|
|
|
708 |
|
|
// use a small angle aproximation for sin and cosine |
709 |
|
|
|
710 |
|
|
angleSqr = angle * angle; |
711 |
|
|
angleSqrOver4 = angleSqr / 4.0; |
712 |
|
|
top = 1.0 - angleSqrOver4; |
713 |
|
|
bottom = 1.0 + angleSqrOver4; |
714 |
|
|
|
715 |
|
|
cosAngle = top / bottom; |
716 |
|
|
sinAngle = angle / bottom; |
717 |
|
|
|
718 |
|
|
rot[axes1][axes1] = cosAngle; |
719 |
|
|
rot[axes2][axes2] = cosAngle; |
720 |
|
|
|
721 |
|
|
rot[axes1][axes2] = sinAngle; |
722 |
|
|
rot[axes2][axes1] = -sinAngle; |
723 |
|
|
|
724 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
725 |
|
|
|
726 |
|
|
for(i=0; i<3; i++){ |
727 |
|
|
ji[i] = 0.0; |
728 |
|
|
for(k=0; k<3; k++){ |
729 |
|
|
ji[i] += rot[i][k] * tempJ[k]; |
730 |
|
|
} |
731 |
|
|
} |
732 |
|
|
|
733 |
|
|
// rotate the Rotation matrix acording to: |
734 |
|
|
// A[][] = A[][] * transpose(rot[][]) |
735 |
|
|
|
736 |
|
|
|
737 |
mmeineke |
561 |
// NOte for as yet unknown reason, we are performing the |
738 |
mmeineke |
558 |
// calculation as: |
739 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
740 |
|
|
|
741 |
|
|
for(i=0; i<3; i++){ |
742 |
|
|
for(j=0; j<3; j++){ |
743 |
mmeineke |
561 |
A[3*j + i] = 0.0; |
744 |
mmeineke |
558 |
for(k=0; k<3; k++){ |
745 |
mmeineke |
561 |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
746 |
mmeineke |
558 |
} |
747 |
|
|
} |
748 |
|
|
} |
749 |
|
|
} |