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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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template<typename T> Integrator<T>::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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template<typename T> Integrator<T>::~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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template<typename T> void Integrator<T>::checkConstraints( void ){ |
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isConstrained = 0; |
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[info->n_SRI]; |
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nConstrained = 0; |
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int constrained = 0; |
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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theArray = (SRI**) molecules[i].getMyBonds(); |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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theArray = (SRI**) molecules[i].getMyBends(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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} |
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if(nConstrained > 0){ |
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isConstrained = 1; |
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if(constrainedA != NULL ) delete[] constrainedA; |
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if(constrainedB != NULL ) delete[] constrainedB; |
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if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
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constrainedA = new int[nConstrained]; |
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constrainedB = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
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for( int i = 0; i < nConstrained; i++){ |
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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} |
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// save oldAtoms to check for lode balanceing later on. |
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oldAtoms = nAtoms; |
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moving = new int[nAtoms]; |
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moved = new int[nAtoms]; |
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oldPos = new double[nAtoms*3]; |
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} |
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delete[] temp_con; |
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} |
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template<typename T> void Integrator<T>::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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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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calcForce(1, 1); |
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if( info->setTemp ){ |
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thermalize(); |
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} |
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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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dumpOut->writeDump( info->getTime() ); |
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statOut->writeStat( info->getTime() ); |
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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( info->getTime() < runTime ){ |
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if( (info->getTime()+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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info->incrTime(dt); |
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if( info->setTemp ){ |
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if( info->getTime() >= currThermal ){ |
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thermalize(); |
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currThermal += thermalTime; |
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} |
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} |
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if( info->getTime() >= currSample ){ |
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dumpOut->writeDump( info->getTime() ); |
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currSample += sampleTime; |
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} |
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if( info->getTime() >= currStatus ){ |
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statOut->writeStat( info->getTime() ); |
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calcPot = 0; |
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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(info->getTime()); |
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delete dumpOut; |
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delete statOut; |
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} |
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template<typename T> void Integrator<T>::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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gezelter |
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if( nConstrained ) constrainA(); |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Succesful moveA\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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// calc forces |
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calcForce(calcPot,calcStress); |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Succesful doForces\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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mmeineke |
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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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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Succesful moveB\n" ); |
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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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tim |
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template<typename T> void Integrator<T>::moveA( void ){ |
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mmeineke |
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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 |
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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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gezelter |
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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 |
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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 |
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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 |
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dAtom->getA(A); |
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dAtom->getI(I); |
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mmeineke |
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// rotate about the x-axis |
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gezelter |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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mmeineke |
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|
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mmeineke |
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// rotate about the y-axis |
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gezelter |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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mmeineke |
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// rotate about the z-axis |
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gezelter |
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angle = dt * ji[2] / I[2][2]; |
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this->rotate( 0, 1, angle, ji, A); |
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mmeineke |
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|
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// rotate about the y-axis |
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gezelter |
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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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mmeineke |
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|
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// rotate about the x-axis |
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gezelter |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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mmeineke |
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mmeineke |
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|
366 |
gezelter |
600 |
dAtom->setJ( ji ); |
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dAtom->setA( A ); |
368 |
mmeineke |
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|
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gezelter |
600 |
} |
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mmeineke |
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} |
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} |
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374 |
tim |
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template<typename T> void Integrator<T>::moveB( void ){ |
375 |
gezelter |
600 |
int i, j; |
376 |
mmeineke |
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DirectionalAtom* dAtom; |
377 |
gezelter |
600 |
double Tb[3], ji[3]; |
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double vel[3], frc[3]; |
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double mass; |
380 |
mmeineke |
558 |
|
381 |
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for( i=0; i<nAtoms; i++ ){ |
382 |
gezelter |
600 |
|
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atoms[i]->getVel( vel ); |
384 |
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atoms[i]->getFrc( frc ); |
385 |
mmeineke |
558 |
|
386 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
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|
388 |
mmeineke |
558 |
// velocity half step |
389 |
gezelter |
600 |
for (j=0; j < 3; j++) |
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vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
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atoms[i]->setVel( vel ); |
393 |
mmeineke |
597 |
|
394 |
mmeineke |
558 |
if( atoms[i]->isDirectional() ){ |
395 |
gezelter |
600 |
|
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mmeineke |
558 |
dAtom = (DirectionalAtom *)atoms[i]; |
397 |
mmeineke |
597 |
|
398 |
gezelter |
600 |
// get and convert the torque to body frame |
399 |
|
|
|
400 |
|
|
dAtom->getTrq( Tb ); |
401 |
mmeineke |
558 |
dAtom->lab2Body( Tb ); |
402 |
gezelter |
600 |
|
403 |
|
|
// get the angular momentum, and propagate a half step |
404 |
|
|
|
405 |
|
|
dAtom->getJ( ji ); |
406 |
|
|
|
407 |
|
|
for (j=0; j < 3; j++) |
408 |
|
|
ji[j] += (dt2 * Tb[j]) * eConvert; |
409 |
mmeineke |
558 |
|
410 |
mmeineke |
597 |
|
411 |
gezelter |
600 |
dAtom->setJ( ji ); |
412 |
mmeineke |
558 |
} |
413 |
|
|
} |
414 |
|
|
} |
415 |
|
|
|
416 |
tim |
645 |
template<typename T> void Integrator<T>::preMove( void ){ |
417 |
gezelter |
600 |
int i, j; |
418 |
|
|
double pos[3]; |
419 |
mmeineke |
558 |
|
420 |
|
|
if( nConstrained ){ |
421 |
mmeineke |
561 |
|
422 |
gezelter |
600 |
for(i=0; i < nAtoms; i++) { |
423 |
|
|
|
424 |
|
|
atoms[i]->getPos( pos ); |
425 |
mmeineke |
558 |
|
426 |
gezelter |
600 |
for (j = 0; j < 3; j++) { |
427 |
|
|
oldPos[3*i + j] = pos[j]; |
428 |
|
|
} |
429 |
|
|
|
430 |
|
|
} |
431 |
|
|
} |
432 |
|
|
} |
433 |
|
|
|
434 |
tim |
645 |
template<typename T> void Integrator<T>::constrainA(){ |
435 |
mmeineke |
558 |
|
436 |
|
|
int i,j,k; |
437 |
|
|
int done; |
438 |
gezelter |
600 |
double posA[3], posB[3]; |
439 |
|
|
double velA[3], velB[3]; |
440 |
mmeineke |
572 |
double pab[3]; |
441 |
|
|
double rab[3]; |
442 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
443 |
mmeineke |
558 |
double rma, rmb; |
444 |
|
|
double dx, dy, dz; |
445 |
mmeineke |
561 |
double rpab; |
446 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
447 |
|
|
double diffsq; |
448 |
|
|
double gab; |
449 |
|
|
int iteration; |
450 |
|
|
|
451 |
gezelter |
600 |
for( i=0; i<nAtoms; i++){ |
452 |
mmeineke |
558 |
moving[i] = 0; |
453 |
|
|
moved[i] = 1; |
454 |
|
|
} |
455 |
mmeineke |
567 |
|
456 |
mmeineke |
558 |
iteration = 0; |
457 |
|
|
done = 0; |
458 |
|
|
while( !done && (iteration < maxIteration )){ |
459 |
|
|
|
460 |
|
|
done = 1; |
461 |
|
|
for(i=0; i<nConstrained; i++){ |
462 |
|
|
|
463 |
|
|
a = constrainedA[i]; |
464 |
|
|
b = constrainedB[i]; |
465 |
mmeineke |
563 |
|
466 |
|
|
ax = (a*3) + 0; |
467 |
|
|
ay = (a*3) + 1; |
468 |
|
|
az = (a*3) + 2; |
469 |
|
|
|
470 |
|
|
bx = (b*3) + 0; |
471 |
|
|
by = (b*3) + 1; |
472 |
|
|
bz = (b*3) + 2; |
473 |
|
|
|
474 |
mmeineke |
558 |
if( moved[a] || moved[b] ){ |
475 |
gezelter |
600 |
|
476 |
|
|
atoms[a]->getPos( posA ); |
477 |
|
|
atoms[b]->getPos( posB ); |
478 |
|
|
|
479 |
|
|
for (j = 0; j < 3; j++ ) |
480 |
|
|
pab[j] = posA[j] - posB[j]; |
481 |
|
|
|
482 |
mmeineke |
567 |
//periodic boundary condition |
483 |
|
|
|
484 |
mmeineke |
572 |
info->wrapVector( pab ); |
485 |
mmeineke |
567 |
|
486 |
mmeineke |
572 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
487 |
|
|
|
488 |
mmeineke |
561 |
rabsq = constrainedDsqr[i]; |
489 |
mmeineke |
567 |
diffsq = rabsq - pabsq; |
490 |
mmeineke |
558 |
|
491 |
|
|
// the original rattle code from alan tidesley |
492 |
mmeineke |
563 |
if (fabs(diffsq) > (tol*rabsq*2)) { |
493 |
mmeineke |
572 |
rab[0] = oldPos[ax] - oldPos[bx]; |
494 |
|
|
rab[1] = oldPos[ay] - oldPos[by]; |
495 |
|
|
rab[2] = oldPos[az] - oldPos[bz]; |
496 |
mmeineke |
567 |
|
497 |
mmeineke |
572 |
info->wrapVector( rab ); |
498 |
mmeineke |
558 |
|
499 |
mmeineke |
572 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
500 |
mmeineke |
567 |
|
501 |
mmeineke |
558 |
rpabsq = rpab * rpab; |
502 |
|
|
|
503 |
|
|
|
504 |
|
|
if (rpabsq < (rabsq * -diffsq)){ |
505 |
mmeineke |
563 |
|
506 |
mmeineke |
558 |
#ifdef IS_MPI |
507 |
|
|
a = atoms[a]->getGlobalIndex(); |
508 |
|
|
b = atoms[b]->getGlobalIndex(); |
509 |
|
|
#endif //is_mpi |
510 |
|
|
sprintf( painCave.errMsg, |
511 |
mmeineke |
563 |
"Constraint failure in constrainA at atom %d and %d.\n", |
512 |
mmeineke |
558 |
a, b ); |
513 |
|
|
painCave.isFatal = 1; |
514 |
|
|
simError(); |
515 |
|
|
} |
516 |
|
|
|
517 |
|
|
rma = 1.0 / atoms[a]->getMass(); |
518 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
519 |
mmeineke |
567 |
|
520 |
mmeineke |
558 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
521 |
mmeineke |
567 |
|
522 |
mmeineke |
572 |
dx = rab[0] * gab; |
523 |
|
|
dy = rab[1] * gab; |
524 |
|
|
dz = rab[2] * gab; |
525 |
mmeineke |
558 |
|
526 |
gezelter |
600 |
posA[0] += rma * dx; |
527 |
|
|
posA[1] += rma * dy; |
528 |
|
|
posA[2] += rma * dz; |
529 |
mmeineke |
558 |
|
530 |
gezelter |
600 |
atoms[a]->setPos( posA ); |
531 |
mmeineke |
558 |
|
532 |
gezelter |
600 |
posB[0] -= rmb * dx; |
533 |
|
|
posB[1] -= rmb * dy; |
534 |
|
|
posB[2] -= rmb * dz; |
535 |
|
|
|
536 |
|
|
atoms[b]->setPos( posB ); |
537 |
|
|
|
538 |
mmeineke |
558 |
dx = dx / dt; |
539 |
|
|
dy = dy / dt; |
540 |
|
|
dz = dz / dt; |
541 |
|
|
|
542 |
gezelter |
600 |
atoms[a]->getVel( velA ); |
543 |
mmeineke |
558 |
|
544 |
gezelter |
600 |
velA[0] += rma * dx; |
545 |
|
|
velA[1] += rma * dy; |
546 |
|
|
velA[2] += rma * dz; |
547 |
mmeineke |
558 |
|
548 |
gezelter |
600 |
atoms[a]->setVel( velA ); |
549 |
|
|
|
550 |
|
|
atoms[b]->getVel( velB ); |
551 |
|
|
|
552 |
|
|
velB[0] -= rmb * dx; |
553 |
|
|
velB[1] -= rmb * dy; |
554 |
|
|
velB[2] -= rmb * dz; |
555 |
|
|
|
556 |
|
|
atoms[b]->setVel( velB ); |
557 |
|
|
|
558 |
mmeineke |
558 |
moving[a] = 1; |
559 |
|
|
moving[b] = 1; |
560 |
|
|
done = 0; |
561 |
|
|
} |
562 |
|
|
} |
563 |
|
|
} |
564 |
|
|
|
565 |
|
|
for(i=0; i<nAtoms; i++){ |
566 |
|
|
|
567 |
|
|
moved[i] = moving[i]; |
568 |
|
|
moving[i] = 0; |
569 |
|
|
} |
570 |
|
|
|
571 |
|
|
iteration++; |
572 |
|
|
} |
573 |
|
|
|
574 |
|
|
if( !done ){ |
575 |
|
|
|
576 |
mmeineke |
561 |
sprintf( painCave.errMsg, |
577 |
mmeineke |
558 |
"Constraint failure in constrainA, too many iterations: %d\n", |
578 |
mmeineke |
561 |
iteration ); |
579 |
mmeineke |
558 |
painCave.isFatal = 1; |
580 |
|
|
simError(); |
581 |
|
|
} |
582 |
|
|
|
583 |
|
|
} |
584 |
|
|
|
585 |
tim |
645 |
template<typename T> void Integrator<T>::constrainB( void ){ |
586 |
mmeineke |
558 |
|
587 |
|
|
int i,j,k; |
588 |
|
|
int done; |
589 |
gezelter |
600 |
double posA[3], posB[3]; |
590 |
|
|
double velA[3], velB[3]; |
591 |
mmeineke |
558 |
double vxab, vyab, vzab; |
592 |
mmeineke |
572 |
double rab[3]; |
593 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
594 |
mmeineke |
558 |
double rma, rmb; |
595 |
|
|
double dx, dy, dz; |
596 |
|
|
double rabsq, pabsq, rvab; |
597 |
|
|
double diffsq; |
598 |
|
|
double gab; |
599 |
|
|
int iteration; |
600 |
|
|
|
601 |
mmeineke |
561 |
for(i=0; i<nAtoms; i++){ |
602 |
mmeineke |
558 |
moving[i] = 0; |
603 |
|
|
moved[i] = 1; |
604 |
|
|
} |
605 |
|
|
|
606 |
|
|
done = 0; |
607 |
mmeineke |
561 |
iteration = 0; |
608 |
mmeineke |
558 |
while( !done && (iteration < maxIteration ) ){ |
609 |
|
|
|
610 |
mmeineke |
567 |
done = 1; |
611 |
|
|
|
612 |
mmeineke |
558 |
for(i=0; i<nConstrained; i++){ |
613 |
|
|
|
614 |
|
|
a = constrainedA[i]; |
615 |
|
|
b = constrainedB[i]; |
616 |
|
|
|
617 |
mmeineke |
567 |
ax = (a*3) + 0; |
618 |
|
|
ay = (a*3) + 1; |
619 |
|
|
az = (a*3) + 2; |
620 |
mmeineke |
563 |
|
621 |
mmeineke |
567 |
bx = (b*3) + 0; |
622 |
|
|
by = (b*3) + 1; |
623 |
|
|
bz = (b*3) + 2; |
624 |
mmeineke |
563 |
|
625 |
mmeineke |
558 |
if( moved[a] || moved[b] ){ |
626 |
|
|
|
627 |
gezelter |
600 |
atoms[a]->getVel( velA ); |
628 |
|
|
atoms[b]->getVel( velB ); |
629 |
|
|
|
630 |
|
|
vxab = velA[0] - velB[0]; |
631 |
|
|
vyab = velA[1] - velB[1]; |
632 |
|
|
vzab = velA[2] - velB[2]; |
633 |
|
|
|
634 |
|
|
atoms[a]->getPos( posA ); |
635 |
|
|
atoms[b]->getPos( posB ); |
636 |
|
|
|
637 |
|
|
for (j = 0; j < 3; j++) |
638 |
|
|
rab[j] = posA[j] - posB[j]; |
639 |
|
|
|
640 |
mmeineke |
572 |
info->wrapVector( rab ); |
641 |
mmeineke |
567 |
|
642 |
mmeineke |
558 |
rma = 1.0 / atoms[a]->getMass(); |
643 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
644 |
|
|
|
645 |
mmeineke |
572 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
646 |
mmeineke |
558 |
|
647 |
mmeineke |
561 |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
648 |
mmeineke |
558 |
|
649 |
|
|
if (fabs(gab) > tol) { |
650 |
|
|
|
651 |
mmeineke |
572 |
dx = rab[0] * gab; |
652 |
|
|
dy = rab[1] * gab; |
653 |
|
|
dz = rab[2] * gab; |
654 |
gezelter |
600 |
|
655 |
|
|
velA[0] += rma * dx; |
656 |
|
|
velA[1] += rma * dy; |
657 |
|
|
velA[2] += rma * dz; |
658 |
mmeineke |
558 |
|
659 |
gezelter |
600 |
atoms[a]->setVel( velA ); |
660 |
|
|
|
661 |
|
|
velB[0] -= rmb * dx; |
662 |
|
|
velB[1] -= rmb * dy; |
663 |
|
|
velB[2] -= rmb * dz; |
664 |
|
|
|
665 |
|
|
atoms[b]->setVel( velB ); |
666 |
mmeineke |
558 |
|
667 |
|
|
moving[a] = 1; |
668 |
|
|
moving[b] = 1; |
669 |
|
|
done = 0; |
670 |
|
|
} |
671 |
|
|
} |
672 |
|
|
} |
673 |
|
|
|
674 |
|
|
for(i=0; i<nAtoms; i++){ |
675 |
|
|
moved[i] = moving[i]; |
676 |
|
|
moving[i] = 0; |
677 |
|
|
} |
678 |
|
|
|
679 |
|
|
iteration++; |
680 |
|
|
} |
681 |
gezelter |
600 |
|
682 |
mmeineke |
558 |
if( !done ){ |
683 |
|
|
|
684 |
|
|
|
685 |
mmeineke |
561 |
sprintf( painCave.errMsg, |
686 |
mmeineke |
558 |
"Constraint failure in constrainB, too many iterations: %d\n", |
687 |
mmeineke |
561 |
iteration ); |
688 |
mmeineke |
558 |
painCave.isFatal = 1; |
689 |
|
|
simError(); |
690 |
|
|
} |
691 |
|
|
|
692 |
|
|
} |
693 |
|
|
|
694 |
tim |
645 |
template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], |
695 |
gezelter |
600 |
double A[3][3] ){ |
696 |
mmeineke |
558 |
|
697 |
|
|
int i,j,k; |
698 |
|
|
double sinAngle; |
699 |
|
|
double cosAngle; |
700 |
|
|
double angleSqr; |
701 |
|
|
double angleSqrOver4; |
702 |
|
|
double top, bottom; |
703 |
|
|
double rot[3][3]; |
704 |
|
|
double tempA[3][3]; |
705 |
|
|
double tempJ[3]; |
706 |
|
|
|
707 |
|
|
// initialize the tempA |
708 |
|
|
|
709 |
|
|
for(i=0; i<3; i++){ |
710 |
|
|
for(j=0; j<3; j++){ |
711 |
gezelter |
600 |
tempA[j][i] = A[i][j]; |
712 |
mmeineke |
558 |
} |
713 |
|
|
} |
714 |
|
|
|
715 |
|
|
// initialize the tempJ |
716 |
|
|
|
717 |
|
|
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
718 |
|
|
|
719 |
|
|
// initalize rot as a unit matrix |
720 |
|
|
|
721 |
|
|
rot[0][0] = 1.0; |
722 |
|
|
rot[0][1] = 0.0; |
723 |
|
|
rot[0][2] = 0.0; |
724 |
|
|
|
725 |
|
|
rot[1][0] = 0.0; |
726 |
|
|
rot[1][1] = 1.0; |
727 |
|
|
rot[1][2] = 0.0; |
728 |
|
|
|
729 |
|
|
rot[2][0] = 0.0; |
730 |
|
|
rot[2][1] = 0.0; |
731 |
|
|
rot[2][2] = 1.0; |
732 |
|
|
|
733 |
|
|
// use a small angle aproximation for sin and cosine |
734 |
|
|
|
735 |
|
|
angleSqr = angle * angle; |
736 |
|
|
angleSqrOver4 = angleSqr / 4.0; |
737 |
|
|
top = 1.0 - angleSqrOver4; |
738 |
|
|
bottom = 1.0 + angleSqrOver4; |
739 |
|
|
|
740 |
|
|
cosAngle = top / bottom; |
741 |
|
|
sinAngle = angle / bottom; |
742 |
|
|
|
743 |
|
|
rot[axes1][axes1] = cosAngle; |
744 |
|
|
rot[axes2][axes2] = cosAngle; |
745 |
|
|
|
746 |
|
|
rot[axes1][axes2] = sinAngle; |
747 |
|
|
rot[axes2][axes1] = -sinAngle; |
748 |
|
|
|
749 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
750 |
|
|
|
751 |
|
|
for(i=0; i<3; i++){ |
752 |
|
|
ji[i] = 0.0; |
753 |
|
|
for(k=0; k<3; k++){ |
754 |
|
|
ji[i] += rot[i][k] * tempJ[k]; |
755 |
|
|
} |
756 |
|
|
} |
757 |
|
|
|
758 |
|
|
// rotate the Rotation matrix acording to: |
759 |
|
|
// A[][] = A[][] * transpose(rot[][]) |
760 |
|
|
|
761 |
|
|
|
762 |
mmeineke |
561 |
// NOte for as yet unknown reason, we are performing the |
763 |
mmeineke |
558 |
// calculation as: |
764 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
765 |
|
|
|
766 |
|
|
for(i=0; i<3; i++){ |
767 |
|
|
for(j=0; j<3; j++){ |
768 |
gezelter |
600 |
A[j][i] = 0.0; |
769 |
mmeineke |
558 |
for(k=0; k<3; k++){ |
770 |
gezelter |
600 |
A[j][i] += tempA[i][k] * rot[j][k]; |
771 |
mmeineke |
558 |
} |
772 |
|
|
} |
773 |
|
|
} |
774 |
|
|
} |
775 |
tim |
677 |
|
776 |
|
|
template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){ |
777 |
|
|
myFF->doForces(calcPot,calcStress); |
778 |
|
|
|
779 |
|
|
} |
780 |
|
|
|
781 |
|
|
template<typename T> void Integrator<T>::thermalize(){ |
782 |
|
|
tStats->velocitize(); |
783 |
|
|
} |