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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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std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
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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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std::cerr << "Is the folowing bond constrained \n"; |
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theArray[j]->printMe(); |
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if(constrained){ |
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std::cerr << "Yes\n"; |
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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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else std::cerr << "No.\n"; |
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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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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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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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std::cerr << currTime << "\n"; |
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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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mmeineke |
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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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mmeineke |
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} |
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mmeineke |
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dumpOut->writeFinal(currTime); |
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mmeineke |
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mmeineke |
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delete dumpOut; |
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delete statOut; |
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mmeineke |
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} |
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void Integrator::integrateStep( int calcPot, int calcStress ){ |
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mmeineke |
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mmeineke |
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// Position full step, and velocity half step |
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mmeineke |
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preMove(); |
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mmeineke |
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moveA(); |
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gezelter |
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if( nConstrained ) constrainA(); |
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mmeineke |
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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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gezelter |
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int i, j; |
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mmeineke |
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DirectionalAtom* dAtom; |
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gezelter |
600 |
double Tb[3], ji[3]; |
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double A[3][3], I[3][3]; |
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mmeineke |
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double angle; |
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gezelter |
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double vel[3], pos[3], frc[3]; |
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double mass; |
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mmeineke |
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for( i=0; i<nAtoms; i++ ){ |
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mmeineke |
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301 |
gezelter |
600 |
atoms[i]->getVel( vel ); |
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atoms[i]->getPos( pos ); |
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atoms[i]->getFrc( frc ); |
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mmeineke |
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gezelter |
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mass = atoms[i]->getMass(); |
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mmeineke |
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gezelter |
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for (j=0; j < 3; j++) { |
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// velocity half step |
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vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
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// position whole step |
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pos[j] += dt * vel[j]; |
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} |
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mmeineke |
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gezelter |
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atoms[i]->setVel( vel ); |
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atoms[i]->setPos( pos ); |
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mmeineke |
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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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gezelter |
600 |
dAtom->getTrq( Tb ); |
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mmeineke |
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dAtom->lab2Body( Tb ); |
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mmeineke |
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|
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mmeineke |
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// get the angular momentum, and propagate a half step |
327 |
gezelter |
600 |
|
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dAtom->getJ( ji ); |
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for (j=0; j < 3; j++) |
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ji[j] += (dt2 * Tb[j]) * eConvert; |
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mmeineke |
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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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gezelter |
600 |
|
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dAtom->getA(A); |
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dAtom->getI(I); |
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339 |
mmeineke |
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// rotate about the x-axis |
340 |
gezelter |
600 |
angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
342 |
mmeineke |
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|
343 |
mmeineke |
558 |
// rotate about the y-axis |
344 |
gezelter |
600 |
angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
346 |
mmeineke |
558 |
|
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// rotate about the z-axis |
348 |
gezelter |
600 |
angle = dt * ji[2] / I[2][2]; |
349 |
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this->rotate( 0, 1, angle, ji, A); |
350 |
mmeineke |
558 |
|
351 |
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// rotate about the y-axis |
352 |
gezelter |
600 |
angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
354 |
mmeineke |
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|
355 |
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// rotate about the x-axis |
356 |
gezelter |
600 |
angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
358 |
mmeineke |
558 |
|
359 |
mmeineke |
597 |
|
360 |
gezelter |
600 |
dAtom->setJ( ji ); |
361 |
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dAtom->setA( A ); |
362 |
mmeineke |
597 |
|
363 |
gezelter |
600 |
} |
364 |
mmeineke |
558 |
} |
365 |
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} |
366 |
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367 |
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368 |
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void Integrator::moveB( void ){ |
369 |
gezelter |
600 |
int i, j; |
370 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
371 |
gezelter |
600 |
double Tb[3], ji[3]; |
372 |
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double vel[3], frc[3]; |
373 |
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double mass; |
374 |
mmeineke |
558 |
|
375 |
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for( i=0; i<nAtoms; i++ ){ |
376 |
gezelter |
600 |
|
377 |
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atoms[i]->getVel( vel ); |
378 |
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atoms[i]->getFrc( frc ); |
379 |
mmeineke |
558 |
|
380 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
381 |
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|
382 |
mmeineke |
558 |
// velocity half step |
383 |
gezelter |
600 |
for (j=0; j < 3; j++) |
384 |
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vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
385 |
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386 |
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atoms[i]->setVel( vel ); |
387 |
mmeineke |
597 |
|
388 |
mmeineke |
558 |
if( atoms[i]->isDirectional() ){ |
389 |
gezelter |
600 |
|
390 |
mmeineke |
558 |
dAtom = (DirectionalAtom *)atoms[i]; |
391 |
mmeineke |
597 |
|
392 |
gezelter |
600 |
// get and convert the torque to body frame |
393 |
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|
394 |
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dAtom->getTrq( Tb ); |
395 |
mmeineke |
558 |
dAtom->lab2Body( Tb ); |
396 |
gezelter |
600 |
|
397 |
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// get the angular momentum, and propagate a half step |
398 |
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399 |
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dAtom->getJ( ji ); |
400 |
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401 |
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for (j=0; j < 3; j++) |
402 |
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ji[j] += (dt2 * Tb[j]) * eConvert; |
403 |
mmeineke |
558 |
|
404 |
mmeineke |
597 |
|
405 |
gezelter |
600 |
dAtom->setJ( ji ); |
406 |
mmeineke |
558 |
} |
407 |
|
|
} |
408 |
|
|
} |
409 |
|
|
|
410 |
|
|
void Integrator::preMove( void ){ |
411 |
gezelter |
600 |
int i, j; |
412 |
|
|
double pos[3]; |
413 |
mmeineke |
558 |
|
414 |
|
|
if( nConstrained ){ |
415 |
mmeineke |
561 |
|
416 |
gezelter |
600 |
for(i=0; i < nAtoms; i++) { |
417 |
|
|
|
418 |
|
|
atoms[i]->getPos( pos ); |
419 |
mmeineke |
558 |
|
420 |
gezelter |
600 |
for (j = 0; j < 3; j++) { |
421 |
|
|
oldPos[3*i + j] = pos[j]; |
422 |
|
|
} |
423 |
|
|
|
424 |
|
|
} |
425 |
|
|
} |
426 |
|
|
} |
427 |
|
|
|
428 |
mmeineke |
558 |
void Integrator::constrainA(){ |
429 |
|
|
|
430 |
|
|
int i,j,k; |
431 |
|
|
int done; |
432 |
gezelter |
600 |
double posA[3], posB[3]; |
433 |
|
|
double velA[3], velB[3]; |
434 |
mmeineke |
572 |
double pab[3]; |
435 |
|
|
double rab[3]; |
436 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
437 |
mmeineke |
558 |
double rma, rmb; |
438 |
|
|
double dx, dy, dz; |
439 |
mmeineke |
561 |
double rpab; |
440 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
441 |
|
|
double diffsq; |
442 |
|
|
double gab; |
443 |
|
|
int iteration; |
444 |
|
|
|
445 |
gezelter |
600 |
for( i=0; i<nAtoms; i++){ |
446 |
mmeineke |
558 |
moving[i] = 0; |
447 |
|
|
moved[i] = 1; |
448 |
|
|
} |
449 |
mmeineke |
567 |
|
450 |
mmeineke |
558 |
iteration = 0; |
451 |
|
|
done = 0; |
452 |
|
|
while( !done && (iteration < maxIteration )){ |
453 |
|
|
|
454 |
|
|
done = 1; |
455 |
|
|
for(i=0; i<nConstrained; i++){ |
456 |
|
|
|
457 |
|
|
a = constrainedA[i]; |
458 |
|
|
b = constrainedB[i]; |
459 |
mmeineke |
563 |
|
460 |
|
|
ax = (a*3) + 0; |
461 |
|
|
ay = (a*3) + 1; |
462 |
|
|
az = (a*3) + 2; |
463 |
|
|
|
464 |
|
|
bx = (b*3) + 0; |
465 |
|
|
by = (b*3) + 1; |
466 |
|
|
bz = (b*3) + 2; |
467 |
|
|
|
468 |
mmeineke |
558 |
if( moved[a] || moved[b] ){ |
469 |
gezelter |
600 |
|
470 |
|
|
atoms[a]->getPos( posA ); |
471 |
|
|
atoms[b]->getPos( posB ); |
472 |
|
|
|
473 |
|
|
for (j = 0; j < 3; j++ ) |
474 |
|
|
pab[j] = posA[j] - posB[j]; |
475 |
|
|
|
476 |
mmeineke |
567 |
//periodic boundary condition |
477 |
|
|
|
478 |
mmeineke |
572 |
info->wrapVector( pab ); |
479 |
mmeineke |
567 |
|
480 |
mmeineke |
572 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
481 |
|
|
|
482 |
mmeineke |
561 |
rabsq = constrainedDsqr[i]; |
483 |
mmeineke |
567 |
diffsq = rabsq - pabsq; |
484 |
mmeineke |
558 |
|
485 |
|
|
// the original rattle code from alan tidesley |
486 |
mmeineke |
563 |
if (fabs(diffsq) > (tol*rabsq*2)) { |
487 |
mmeineke |
572 |
rab[0] = oldPos[ax] - oldPos[bx]; |
488 |
|
|
rab[1] = oldPos[ay] - oldPos[by]; |
489 |
|
|
rab[2] = oldPos[az] - oldPos[bz]; |
490 |
mmeineke |
567 |
|
491 |
mmeineke |
572 |
info->wrapVector( rab ); |
492 |
mmeineke |
558 |
|
493 |
mmeineke |
572 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
494 |
mmeineke |
567 |
|
495 |
mmeineke |
558 |
rpabsq = rpab * rpab; |
496 |
|
|
|
497 |
|
|
|
498 |
|
|
if (rpabsq < (rabsq * -diffsq)){ |
499 |
mmeineke |
563 |
|
500 |
mmeineke |
558 |
#ifdef IS_MPI |
501 |
|
|
a = atoms[a]->getGlobalIndex(); |
502 |
|
|
b = atoms[b]->getGlobalIndex(); |
503 |
|
|
#endif //is_mpi |
504 |
|
|
sprintf( painCave.errMsg, |
505 |
mmeineke |
563 |
"Constraint failure in constrainA at atom %d and %d.\n", |
506 |
mmeineke |
558 |
a, b ); |
507 |
|
|
painCave.isFatal = 1; |
508 |
|
|
simError(); |
509 |
|
|
} |
510 |
|
|
|
511 |
|
|
rma = 1.0 / atoms[a]->getMass(); |
512 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
513 |
mmeineke |
567 |
|
514 |
mmeineke |
558 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
515 |
mmeineke |
567 |
|
516 |
mmeineke |
572 |
dx = rab[0] * gab; |
517 |
|
|
dy = rab[1] * gab; |
518 |
|
|
dz = rab[2] * gab; |
519 |
mmeineke |
558 |
|
520 |
gezelter |
600 |
posA[0] += rma * dx; |
521 |
|
|
posA[1] += rma * dy; |
522 |
|
|
posA[2] += rma * dz; |
523 |
mmeineke |
558 |
|
524 |
gezelter |
600 |
atoms[a]->setPos( posA ); |
525 |
mmeineke |
558 |
|
526 |
gezelter |
600 |
posB[0] -= rmb * dx; |
527 |
|
|
posB[1] -= rmb * dy; |
528 |
|
|
posB[2] -= rmb * dz; |
529 |
|
|
|
530 |
|
|
atoms[b]->setPos( posB ); |
531 |
|
|
|
532 |
mmeineke |
558 |
dx = dx / dt; |
533 |
|
|
dy = dy / dt; |
534 |
|
|
dz = dz / dt; |
535 |
|
|
|
536 |
gezelter |
600 |
atoms[a]->getVel( velA ); |
537 |
mmeineke |
558 |
|
538 |
gezelter |
600 |
velA[0] += rma * dx; |
539 |
|
|
velA[1] += rma * dy; |
540 |
|
|
velA[2] += rma * dz; |
541 |
mmeineke |
558 |
|
542 |
gezelter |
600 |
atoms[a]->setVel( velA ); |
543 |
|
|
|
544 |
|
|
atoms[b]->getVel( velB ); |
545 |
|
|
|
546 |
|
|
velB[0] -= rmb * dx; |
547 |
|
|
velB[1] -= rmb * dy; |
548 |
|
|
velB[2] -= rmb * dz; |
549 |
|
|
|
550 |
|
|
atoms[b]->setVel( velB ); |
551 |
|
|
|
552 |
mmeineke |
558 |
moving[a] = 1; |
553 |
|
|
moving[b] = 1; |
554 |
|
|
done = 0; |
555 |
|
|
} |
556 |
|
|
} |
557 |
|
|
} |
558 |
|
|
|
559 |
|
|
for(i=0; i<nAtoms; i++){ |
560 |
|
|
|
561 |
|
|
moved[i] = moving[i]; |
562 |
|
|
moving[i] = 0; |
563 |
|
|
} |
564 |
|
|
|
565 |
|
|
iteration++; |
566 |
|
|
} |
567 |
|
|
|
568 |
|
|
if( !done ){ |
569 |
|
|
|
570 |
mmeineke |
561 |
sprintf( painCave.errMsg, |
571 |
mmeineke |
558 |
"Constraint failure in constrainA, too many iterations: %d\n", |
572 |
mmeineke |
561 |
iteration ); |
573 |
mmeineke |
558 |
painCave.isFatal = 1; |
574 |
|
|
simError(); |
575 |
|
|
} |
576 |
|
|
|
577 |
|
|
} |
578 |
|
|
|
579 |
|
|
void Integrator::constrainB( void ){ |
580 |
|
|
|
581 |
|
|
int i,j,k; |
582 |
|
|
int done; |
583 |
gezelter |
600 |
double posA[3], posB[3]; |
584 |
|
|
double velA[3], velB[3]; |
585 |
mmeineke |
558 |
double vxab, vyab, vzab; |
586 |
mmeineke |
572 |
double rab[3]; |
587 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
588 |
mmeineke |
558 |
double rma, rmb; |
589 |
|
|
double dx, dy, dz; |
590 |
|
|
double rabsq, pabsq, rvab; |
591 |
|
|
double diffsq; |
592 |
|
|
double gab; |
593 |
|
|
int iteration; |
594 |
|
|
|
595 |
mmeineke |
561 |
for(i=0; i<nAtoms; i++){ |
596 |
mmeineke |
558 |
moving[i] = 0; |
597 |
|
|
moved[i] = 1; |
598 |
|
|
} |
599 |
|
|
|
600 |
|
|
done = 0; |
601 |
mmeineke |
561 |
iteration = 0; |
602 |
mmeineke |
558 |
while( !done && (iteration < maxIteration ) ){ |
603 |
|
|
|
604 |
mmeineke |
567 |
done = 1; |
605 |
|
|
|
606 |
mmeineke |
558 |
for(i=0; i<nConstrained; i++){ |
607 |
|
|
|
608 |
|
|
a = constrainedA[i]; |
609 |
|
|
b = constrainedB[i]; |
610 |
|
|
|
611 |
mmeineke |
567 |
ax = (a*3) + 0; |
612 |
|
|
ay = (a*3) + 1; |
613 |
|
|
az = (a*3) + 2; |
614 |
mmeineke |
563 |
|
615 |
mmeineke |
567 |
bx = (b*3) + 0; |
616 |
|
|
by = (b*3) + 1; |
617 |
|
|
bz = (b*3) + 2; |
618 |
mmeineke |
563 |
|
619 |
mmeineke |
558 |
if( moved[a] || moved[b] ){ |
620 |
|
|
|
621 |
gezelter |
600 |
atoms[a]->getVel( velA ); |
622 |
|
|
atoms[b]->getVel( velB ); |
623 |
|
|
|
624 |
|
|
vxab = velA[0] - velB[0]; |
625 |
|
|
vyab = velA[1] - velB[1]; |
626 |
|
|
vzab = velA[2] - velB[2]; |
627 |
|
|
|
628 |
|
|
atoms[a]->getPos( posA ); |
629 |
|
|
atoms[b]->getPos( posB ); |
630 |
|
|
|
631 |
|
|
for (j = 0; j < 3; j++) |
632 |
|
|
rab[j] = posA[j] - posB[j]; |
633 |
|
|
|
634 |
mmeineke |
572 |
info->wrapVector( rab ); |
635 |
mmeineke |
567 |
|
636 |
mmeineke |
558 |
rma = 1.0 / atoms[a]->getMass(); |
637 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
638 |
|
|
|
639 |
mmeineke |
572 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
640 |
mmeineke |
558 |
|
641 |
mmeineke |
561 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
642 |
mmeineke |
558 |
|
643 |
|
|
if (fabs(gab) > tol) { |
644 |
|
|
|
645 |
mmeineke |
572 |
dx = rab[0] * gab; |
646 |
|
|
dy = rab[1] * gab; |
647 |
|
|
dz = rab[2] * gab; |
648 |
gezelter |
600 |
|
649 |
|
|
velA[0] += rma * dx; |
650 |
|
|
velA[1] += rma * dy; |
651 |
|
|
velA[2] += rma * dz; |
652 |
mmeineke |
558 |
|
653 |
gezelter |
600 |
atoms[a]->setVel( velA ); |
654 |
|
|
|
655 |
|
|
velB[0] -= rmb * dx; |
656 |
|
|
velB[1] -= rmb * dy; |
657 |
|
|
velB[2] -= rmb * dz; |
658 |
|
|
|
659 |
|
|
atoms[b]->setVel( velB ); |
660 |
mmeineke |
558 |
|
661 |
|
|
moving[a] = 1; |
662 |
|
|
moving[b] = 1; |
663 |
|
|
done = 0; |
664 |
|
|
} |
665 |
|
|
} |
666 |
|
|
} |
667 |
|
|
|
668 |
|
|
for(i=0; i<nAtoms; i++){ |
669 |
|
|
moved[i] = moving[i]; |
670 |
|
|
moving[i] = 0; |
671 |
|
|
} |
672 |
|
|
|
673 |
|
|
iteration++; |
674 |
|
|
} |
675 |
gezelter |
600 |
|
676 |
mmeineke |
558 |
if( !done ){ |
677 |
|
|
|
678 |
|
|
|
679 |
mmeineke |
561 |
sprintf( painCave.errMsg, |
680 |
mmeineke |
558 |
"Constraint failure in constrainB, too many iterations: %d\n", |
681 |
mmeineke |
561 |
iteration ); |
682 |
mmeineke |
558 |
painCave.isFatal = 1; |
683 |
|
|
simError(); |
684 |
|
|
} |
685 |
|
|
|
686 |
|
|
} |
687 |
|
|
|
688 |
|
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
689 |
gezelter |
600 |
double A[3][3] ){ |
690 |
mmeineke |
558 |
|
691 |
|
|
int i,j,k; |
692 |
|
|
double sinAngle; |
693 |
|
|
double cosAngle; |
694 |
|
|
double angleSqr; |
695 |
|
|
double angleSqrOver4; |
696 |
|
|
double top, bottom; |
697 |
|
|
double rot[3][3]; |
698 |
|
|
double tempA[3][3]; |
699 |
|
|
double tempJ[3]; |
700 |
|
|
|
701 |
|
|
// initialize the tempA |
702 |
|
|
|
703 |
|
|
for(i=0; i<3; i++){ |
704 |
|
|
for(j=0; j<3; j++){ |
705 |
gezelter |
600 |
tempA[j][i] = A[i][j]; |
706 |
mmeineke |
558 |
} |
707 |
|
|
} |
708 |
|
|
|
709 |
|
|
// initialize the tempJ |
710 |
|
|
|
711 |
|
|
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
712 |
|
|
|
713 |
|
|
// initalize rot as a unit matrix |
714 |
|
|
|
715 |
|
|
rot[0][0] = 1.0; |
716 |
|
|
rot[0][1] = 0.0; |
717 |
|
|
rot[0][2] = 0.0; |
718 |
|
|
|
719 |
|
|
rot[1][0] = 0.0; |
720 |
|
|
rot[1][1] = 1.0; |
721 |
|
|
rot[1][2] = 0.0; |
722 |
|
|
|
723 |
|
|
rot[2][0] = 0.0; |
724 |
|
|
rot[2][1] = 0.0; |
725 |
|
|
rot[2][2] = 1.0; |
726 |
|
|
|
727 |
|
|
// use a small angle aproximation for sin and cosine |
728 |
|
|
|
729 |
|
|
angleSqr = angle * angle; |
730 |
|
|
angleSqrOver4 = angleSqr / 4.0; |
731 |
|
|
top = 1.0 - angleSqrOver4; |
732 |
|
|
bottom = 1.0 + angleSqrOver4; |
733 |
|
|
|
734 |
|
|
cosAngle = top / bottom; |
735 |
|
|
sinAngle = angle / bottom; |
736 |
|
|
|
737 |
|
|
rot[axes1][axes1] = cosAngle; |
738 |
|
|
rot[axes2][axes2] = cosAngle; |
739 |
|
|
|
740 |
|
|
rot[axes1][axes2] = sinAngle; |
741 |
|
|
rot[axes2][axes1] = -sinAngle; |
742 |
|
|
|
743 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
744 |
|
|
|
745 |
|
|
for(i=0; i<3; i++){ |
746 |
|
|
ji[i] = 0.0; |
747 |
|
|
for(k=0; k<3; k++){ |
748 |
|
|
ji[i] += rot[i][k] * tempJ[k]; |
749 |
|
|
} |
750 |
|
|
} |
751 |
|
|
|
752 |
|
|
// rotate the Rotation matrix acording to: |
753 |
|
|
// A[][] = A[][] * transpose(rot[][]) |
754 |
|
|
|
755 |
|
|
|
756 |
mmeineke |
561 |
// NOte for as yet unknown reason, we are performing the |
757 |
mmeineke |
558 |
// calculation as: |
758 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
759 |
|
|
|
760 |
|
|
for(i=0; i<3; i++){ |
761 |
|
|
for(j=0; j<3; j++){ |
762 |
gezelter |
600 |
A[j][i] = 0.0; |
763 |
mmeineke |
558 |
for(k=0; k<3; k++){ |
764 |
gezelter |
600 |
A[j][i] += tempA[i][k] * rot[j][k]; |
765 |
mmeineke |
558 |
} |
766 |
|
|
} |
767 |
|
|
} |
768 |
|
|
} |