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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, |
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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){ |
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delete info->the_integrator; |
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} |
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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) |
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delete[] constrainedA; |
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if (constrainedB != NULL) |
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delete[] constrainedB; |
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if (constrainedDsqr != NULL) |
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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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|
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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 resetTime = info->resetTime; |
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double currSample; |
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double currThermal; |
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double currStatus; |
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double currReset; |
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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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readyCheck(); |
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// initialize the forces before the first step |
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calcForce(1, 1); |
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if (nConstrained){ |
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preMove(); |
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constrainA(); |
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calcForce(1, 1); |
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constrainB(); |
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} |
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tim |
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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 + info->getTime(); |
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currThermal = thermalTime+ info->getTime(); |
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currStatus = statusTime + info->getTime(); |
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currReset = resetTime + info->getTime(); |
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dumpOut->writeDump(info->getTime()); |
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statOut->writeStat(info->getTime()); |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "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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mmeineke |
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mmeineke |
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if (info->resetIntegrator){ |
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if (info->getTime() >= currReset){ |
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this->resetIntegrator(); |
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currReset += resetTime; |
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} |
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} |
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mmeineke |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "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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mmeineke |
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dumpOut->writeFinal(info->getTime()); |
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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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template<typename T> void Integrator<T>::integrateStep(int calcPot, |
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int calcStress){ |
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mmeineke |
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// Position full step, and velocity half step |
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tim |
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preMove(); |
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mmeineke |
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moveA(); |
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tim |
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mmeineke |
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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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tim |
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mmeineke |
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// calc forces |
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tim |
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calcForce(calcPot, calcStress); |
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mmeineke |
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mmeineke |
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#ifdef IS_MPI |
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tim |
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strcpy(checkPointMsg, "Succesful doForces\n"); |
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mmeineke |
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MPIcheckPoint(); |
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#endif // is_mpi |
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tim |
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|
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mmeineke |
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// finish the velocity half step |
285 |
tim |
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|
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mmeineke |
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moveB(); |
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tim |
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mmeineke |
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mmeineke |
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#ifdef IS_MPI |
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tim |
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strcpy(checkPointMsg, "Succesful moveB\n"); |
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mmeineke |
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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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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 vel[3], pos[3], frc[3]; |
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double mass; |
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mmeineke |
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|
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tim |
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for (i = 0; i < nAtoms; i++){ |
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atoms[i]->getVel(vel); |
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atoms[i]->getPos(pos); |
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atoms[i]->getFrc(frc); |
308 |
mmeineke |
567 |
|
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gezelter |
600 |
mass = atoms[i]->getMass(); |
310 |
mmeineke |
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|
311 |
tim |
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for (j = 0; j < 3; j++){ |
312 |
gezelter |
600 |
// velocity half step |
313 |
tim |
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vel[j] += (dt2 * frc[j] / mass) * eConvert; |
314 |
gezelter |
600 |
// position whole step |
315 |
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pos[j] += dt * vel[j]; |
316 |
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} |
317 |
mmeineke |
594 |
|
318 |
tim |
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atoms[i]->setVel(vel); |
319 |
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atoms[i]->setPos(pos); |
320 |
gezelter |
600 |
|
321 |
tim |
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if (atoms[i]->isDirectional()){ |
322 |
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dAtom = (DirectionalAtom *) atoms[i]; |
323 |
mmeineke |
558 |
|
324 |
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// get and convert the torque to body frame |
325 |
mmeineke |
597 |
|
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tim |
725 |
dAtom->getTrq(Tb); |
327 |
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dAtom->lab2Body(Tb); |
328 |
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329 |
mmeineke |
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// get the angular momentum, and propagate a half step |
330 |
gezelter |
600 |
|
331 |
tim |
725 |
dAtom->getJ(ji); |
332 |
gezelter |
600 |
|
333 |
tim |
725 |
for (j = 0; j < 3; j++) |
334 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
335 |
tim |
725 |
|
336 |
mmeineke |
778 |
this->rotationPropagation( dAtom, ji ); |
337 |
gezelter |
600 |
|
338 |
tim |
725 |
dAtom->setJ(ji); |
339 |
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} |
340 |
mmeineke |
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} |
341 |
mmeineke |
768 |
|
342 |
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if (nConstrained){ |
343 |
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constrainA(); |
344 |
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} |
345 |
mmeineke |
558 |
} |
346 |
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347 |
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348 |
tim |
725 |
template<typename T> void Integrator<T>::moveB(void){ |
349 |
gezelter |
600 |
int i, j; |
350 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
351 |
gezelter |
600 |
double Tb[3], ji[3]; |
352 |
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double vel[3], frc[3]; |
353 |
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double mass; |
354 |
mmeineke |
558 |
|
355 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
356 |
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atoms[i]->getVel(vel); |
357 |
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atoms[i]->getFrc(frc); |
358 |
mmeineke |
558 |
|
359 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
360 |
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|
361 |
mmeineke |
558 |
// velocity half step |
362 |
tim |
725 |
for (j = 0; j < 3; j++) |
363 |
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vel[j] += (dt2 * frc[j] / mass) * eConvert; |
364 |
gezelter |
600 |
|
365 |
tim |
725 |
atoms[i]->setVel(vel); |
366 |
mmeineke |
597 |
|
367 |
tim |
725 |
if (atoms[i]->isDirectional()){ |
368 |
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dAtom = (DirectionalAtom *) atoms[i]; |
369 |
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|
370 |
gezelter |
600 |
// get and convert the torque to body frame |
371 |
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|
372 |
tim |
725 |
dAtom->getTrq(Tb); |
373 |
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dAtom->lab2Body(Tb); |
374 |
gezelter |
600 |
|
375 |
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// get the angular momentum, and propagate a half step |
376 |
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|
377 |
tim |
725 |
dAtom->getJ(ji); |
378 |
gezelter |
600 |
|
379 |
tim |
725 |
for (j = 0; j < 3; j++) |
380 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
381 |
mmeineke |
597 |
|
382 |
tim |
725 |
|
383 |
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dAtom->setJ(ji); |
384 |
mmeineke |
558 |
} |
385 |
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} |
386 |
mmeineke |
768 |
|
387 |
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if (nConstrained){ |
388 |
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constrainB(); |
389 |
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} |
390 |
mmeineke |
558 |
} |
391 |
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|
392 |
tim |
725 |
template<typename T> void Integrator<T>::preMove(void){ |
393 |
gezelter |
600 |
int i, j; |
394 |
|
|
double pos[3]; |
395 |
mmeineke |
558 |
|
396 |
tim |
725 |
if (nConstrained){ |
397 |
|
|
for (i = 0; i < nAtoms; i++){ |
398 |
|
|
atoms[i]->getPos(pos); |
399 |
mmeineke |
561 |
|
400 |
tim |
725 |
for (j = 0; j < 3; j++){ |
401 |
|
|
oldPos[3 * i + j] = pos[j]; |
402 |
gezelter |
600 |
} |
403 |
|
|
} |
404 |
tim |
725 |
} |
405 |
gezelter |
600 |
} |
406 |
|
|
|
407 |
tim |
645 |
template<typename T> void Integrator<T>::constrainA(){ |
408 |
tim |
725 |
int i, j, k; |
409 |
mmeineke |
558 |
int done; |
410 |
gezelter |
600 |
double posA[3], posB[3]; |
411 |
|
|
double velA[3], velB[3]; |
412 |
mmeineke |
572 |
double pab[3]; |
413 |
|
|
double rab[3]; |
414 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
415 |
mmeineke |
558 |
double rma, rmb; |
416 |
|
|
double dx, dy, dz; |
417 |
mmeineke |
561 |
double rpab; |
418 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
419 |
|
|
double diffsq; |
420 |
|
|
double gab; |
421 |
|
|
int iteration; |
422 |
|
|
|
423 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
424 |
mmeineke |
558 |
moving[i] = 0; |
425 |
tim |
725 |
moved[i] = 1; |
426 |
mmeineke |
558 |
} |
427 |
mmeineke |
567 |
|
428 |
mmeineke |
558 |
iteration = 0; |
429 |
|
|
done = 0; |
430 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
431 |
mmeineke |
558 |
done = 1; |
432 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
433 |
mmeineke |
558 |
a = constrainedA[i]; |
434 |
|
|
b = constrainedB[i]; |
435 |
mmeineke |
563 |
|
436 |
tim |
725 |
ax = (a * 3) + 0; |
437 |
|
|
ay = (a * 3) + 1; |
438 |
|
|
az = (a * 3) + 2; |
439 |
mmeineke |
563 |
|
440 |
tim |
725 |
bx = (b * 3) + 0; |
441 |
|
|
by = (b * 3) + 1; |
442 |
|
|
bz = (b * 3) + 2; |
443 |
|
|
|
444 |
|
|
if (moved[a] || moved[b]){ |
445 |
|
|
atoms[a]->getPos(posA); |
446 |
|
|
atoms[b]->getPos(posB); |
447 |
|
|
|
448 |
|
|
for (j = 0; j < 3; j++) |
449 |
gezelter |
600 |
pab[j] = posA[j] - posB[j]; |
450 |
mmeineke |
567 |
|
451 |
tim |
725 |
//periodic boundary condition |
452 |
mmeineke |
567 |
|
453 |
tim |
725 |
info->wrapVector(pab); |
454 |
mmeineke |
572 |
|
455 |
tim |
725 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
456 |
mmeineke |
558 |
|
457 |
tim |
725 |
rabsq = constrainedDsqr[i]; |
458 |
|
|
diffsq = rabsq - pabsq; |
459 |
mmeineke |
567 |
|
460 |
tim |
725 |
// the original rattle code from alan tidesley |
461 |
|
|
if (fabs(diffsq) > (tol * rabsq * 2)){ |
462 |
|
|
rab[0] = oldPos[ax] - oldPos[bx]; |
463 |
|
|
rab[1] = oldPos[ay] - oldPos[by]; |
464 |
|
|
rab[2] = oldPos[az] - oldPos[bz]; |
465 |
mmeineke |
558 |
|
466 |
tim |
725 |
info->wrapVector(rab); |
467 |
mmeineke |
567 |
|
468 |
tim |
725 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
469 |
mmeineke |
558 |
|
470 |
tim |
725 |
rpabsq = rpab * rpab; |
471 |
mmeineke |
558 |
|
472 |
mmeineke |
563 |
|
473 |
tim |
725 |
if (rpabsq < (rabsq * -diffsq)){ |
474 |
mmeineke |
558 |
#ifdef IS_MPI |
475 |
tim |
725 |
a = atoms[a]->getGlobalIndex(); |
476 |
|
|
b = atoms[b]->getGlobalIndex(); |
477 |
mmeineke |
558 |
#endif //is_mpi |
478 |
tim |
725 |
sprintf(painCave.errMsg, |
479 |
|
|
"Constraint failure in constrainA at atom %d and %d.\n", a, |
480 |
|
|
b); |
481 |
|
|
painCave.isFatal = 1; |
482 |
|
|
simError(); |
483 |
|
|
} |
484 |
mmeineke |
558 |
|
485 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
486 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
487 |
mmeineke |
567 |
|
488 |
tim |
725 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
489 |
mmeineke |
567 |
|
490 |
mmeineke |
572 |
dx = rab[0] * gab; |
491 |
|
|
dy = rab[1] * gab; |
492 |
|
|
dz = rab[2] * gab; |
493 |
mmeineke |
558 |
|
494 |
tim |
725 |
posA[0] += rma * dx; |
495 |
|
|
posA[1] += rma * dy; |
496 |
|
|
posA[2] += rma * dz; |
497 |
mmeineke |
558 |
|
498 |
tim |
725 |
atoms[a]->setPos(posA); |
499 |
mmeineke |
558 |
|
500 |
tim |
725 |
posB[0] -= rmb * dx; |
501 |
|
|
posB[1] -= rmb * dy; |
502 |
|
|
posB[2] -= rmb * dz; |
503 |
gezelter |
600 |
|
504 |
tim |
725 |
atoms[b]->setPos(posB); |
505 |
gezelter |
600 |
|
506 |
mmeineke |
558 |
dx = dx / dt; |
507 |
|
|
dy = dy / dt; |
508 |
|
|
dz = dz / dt; |
509 |
|
|
|
510 |
tim |
725 |
atoms[a]->getVel(velA); |
511 |
mmeineke |
558 |
|
512 |
tim |
725 |
velA[0] += rma * dx; |
513 |
|
|
velA[1] += rma * dy; |
514 |
|
|
velA[2] += rma * dz; |
515 |
mmeineke |
558 |
|
516 |
tim |
725 |
atoms[a]->setVel(velA); |
517 |
gezelter |
600 |
|
518 |
tim |
725 |
atoms[b]->getVel(velB); |
519 |
gezelter |
600 |
|
520 |
tim |
725 |
velB[0] -= rmb * dx; |
521 |
|
|
velB[1] -= rmb * dy; |
522 |
|
|
velB[2] -= rmb * dz; |
523 |
gezelter |
600 |
|
524 |
tim |
725 |
atoms[b]->setVel(velB); |
525 |
gezelter |
600 |
|
526 |
tim |
725 |
moving[a] = 1; |
527 |
|
|
moving[b] = 1; |
528 |
|
|
done = 0; |
529 |
|
|
} |
530 |
mmeineke |
558 |
} |
531 |
|
|
} |
532 |
tim |
725 |
|
533 |
|
|
for (i = 0; i < nAtoms; i++){ |
534 |
mmeineke |
558 |
moved[i] = moving[i]; |
535 |
|
|
moving[i] = 0; |
536 |
|
|
} |
537 |
|
|
|
538 |
|
|
iteration++; |
539 |
|
|
} |
540 |
|
|
|
541 |
tim |
725 |
if (!done){ |
542 |
|
|
sprintf(painCave.errMsg, |
543 |
|
|
"Constraint failure in constrainA, too many iterations: %d\n", |
544 |
|
|
iteration); |
545 |
mmeineke |
558 |
painCave.isFatal = 1; |
546 |
|
|
simError(); |
547 |
|
|
} |
548 |
mmeineke |
768 |
|
549 |
mmeineke |
558 |
} |
550 |
|
|
|
551 |
tim |
725 |
template<typename T> void Integrator<T>::constrainB(void){ |
552 |
|
|
int i, j, k; |
553 |
mmeineke |
558 |
int done; |
554 |
gezelter |
600 |
double posA[3], posB[3]; |
555 |
|
|
double velA[3], velB[3]; |
556 |
mmeineke |
558 |
double vxab, vyab, vzab; |
557 |
mmeineke |
572 |
double rab[3]; |
558 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
559 |
mmeineke |
558 |
double rma, rmb; |
560 |
|
|
double dx, dy, dz; |
561 |
|
|
double rabsq, pabsq, rvab; |
562 |
|
|
double diffsq; |
563 |
|
|
double gab; |
564 |
|
|
int iteration; |
565 |
|
|
|
566 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
567 |
mmeineke |
558 |
moving[i] = 0; |
568 |
|
|
moved[i] = 1; |
569 |
|
|
} |
570 |
|
|
|
571 |
|
|
done = 0; |
572 |
mmeineke |
561 |
iteration = 0; |
573 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
574 |
mmeineke |
567 |
done = 1; |
575 |
|
|
|
576 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
577 |
mmeineke |
558 |
a = constrainedA[i]; |
578 |
|
|
b = constrainedB[i]; |
579 |
|
|
|
580 |
tim |
725 |
ax = (a * 3) + 0; |
581 |
|
|
ay = (a * 3) + 1; |
582 |
|
|
az = (a * 3) + 2; |
583 |
mmeineke |
563 |
|
584 |
tim |
725 |
bx = (b * 3) + 0; |
585 |
|
|
by = (b * 3) + 1; |
586 |
|
|
bz = (b * 3) + 2; |
587 |
mmeineke |
563 |
|
588 |
tim |
725 |
if (moved[a] || moved[b]){ |
589 |
|
|
atoms[a]->getVel(velA); |
590 |
|
|
atoms[b]->getVel(velB); |
591 |
mmeineke |
558 |
|
592 |
tim |
725 |
vxab = velA[0] - velB[0]; |
593 |
|
|
vyab = velA[1] - velB[1]; |
594 |
|
|
vzab = velA[2] - velB[2]; |
595 |
gezelter |
600 |
|
596 |
tim |
725 |
atoms[a]->getPos(posA); |
597 |
|
|
atoms[b]->getPos(posB); |
598 |
gezelter |
600 |
|
599 |
tim |
725 |
for (j = 0; j < 3; j++) |
600 |
gezelter |
600 |
rab[j] = posA[j] - posB[j]; |
601 |
mmeineke |
558 |
|
602 |
tim |
725 |
info->wrapVector(rab); |
603 |
mmeineke |
558 |
|
604 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
605 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
606 |
mmeineke |
558 |
|
607 |
tim |
725 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
608 |
gezelter |
600 |
|
609 |
tim |
725 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
610 |
gezelter |
600 |
|
611 |
tim |
725 |
if (fabs(gab) > tol){ |
612 |
|
|
dx = rab[0] * gab; |
613 |
|
|
dy = rab[1] * gab; |
614 |
|
|
dz = rab[2] * gab; |
615 |
|
|
|
616 |
|
|
velA[0] += rma * dx; |
617 |
|
|
velA[1] += rma * dy; |
618 |
|
|
velA[2] += rma * dz; |
619 |
|
|
|
620 |
|
|
atoms[a]->setVel(velA); |
621 |
|
|
|
622 |
|
|
velB[0] -= rmb * dx; |
623 |
|
|
velB[1] -= rmb * dy; |
624 |
|
|
velB[2] -= rmb * dz; |
625 |
|
|
|
626 |
|
|
atoms[b]->setVel(velB); |
627 |
|
|
|
628 |
|
|
moving[a] = 1; |
629 |
|
|
moving[b] = 1; |
630 |
|
|
done = 0; |
631 |
|
|
} |
632 |
mmeineke |
558 |
} |
633 |
|
|
} |
634 |
|
|
|
635 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
636 |
mmeineke |
558 |
moved[i] = moving[i]; |
637 |
|
|
moving[i] = 0; |
638 |
|
|
} |
639 |
tim |
725 |
|
640 |
mmeineke |
558 |
iteration++; |
641 |
|
|
} |
642 |
|
|
|
643 |
tim |
725 |
if (!done){ |
644 |
|
|
sprintf(painCave.errMsg, |
645 |
|
|
"Constraint failure in constrainB, too many iterations: %d\n", |
646 |
|
|
iteration); |
647 |
mmeineke |
558 |
painCave.isFatal = 1; |
648 |
|
|
simError(); |
649 |
tim |
725 |
} |
650 |
mmeineke |
558 |
} |
651 |
|
|
|
652 |
mmeineke |
778 |
template<typename T> void Integrator<T>::rotationPropagation |
653 |
|
|
( DirectionalAtom* dAtom, double ji[3] ){ |
654 |
|
|
|
655 |
|
|
double angle; |
656 |
|
|
double A[3][3], I[3][3]; |
657 |
|
|
|
658 |
|
|
// use the angular velocities to propagate the rotation matrix a |
659 |
|
|
// full time step |
660 |
|
|
|
661 |
|
|
dAtom->getA(A); |
662 |
|
|
dAtom->getI(I); |
663 |
|
|
|
664 |
|
|
// rotate about the x-axis |
665 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
666 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
667 |
|
|
|
668 |
|
|
// rotate about the y-axis |
669 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
670 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
671 |
|
|
|
672 |
|
|
// rotate about the z-axis |
673 |
|
|
angle = dt * ji[2] / I[2][2]; |
674 |
|
|
this->rotate( 0, 1, angle, ji, A); |
675 |
|
|
|
676 |
|
|
// rotate about the y-axis |
677 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
678 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
679 |
|
|
|
680 |
|
|
// rotate about the x-axis |
681 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
682 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
683 |
|
|
|
684 |
|
|
dAtom->setA( A ); |
685 |
|
|
} |
686 |
|
|
|
687 |
tim |
725 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
688 |
|
|
double angle, double ji[3], |
689 |
|
|
double A[3][3]){ |
690 |
|
|
int i, j, k; |
691 |
mmeineke |
558 |
double sinAngle; |
692 |
|
|
double cosAngle; |
693 |
|
|
double angleSqr; |
694 |
|
|
double angleSqrOver4; |
695 |
|
|
double top, bottom; |
696 |
|
|
double rot[3][3]; |
697 |
|
|
double tempA[3][3]; |
698 |
|
|
double tempJ[3]; |
699 |
|
|
|
700 |
|
|
// initialize the tempA |
701 |
|
|
|
702 |
tim |
725 |
for (i = 0; i < 3; i++){ |
703 |
|
|
for (j = 0; j < 3; j++){ |
704 |
gezelter |
600 |
tempA[j][i] = A[i][j]; |
705 |
mmeineke |
558 |
} |
706 |
|
|
} |
707 |
|
|
|
708 |
|
|
// initialize the tempJ |
709 |
|
|
|
710 |
tim |
725 |
for (i = 0; i < 3; i++) |
711 |
|
|
tempJ[i] = ji[i]; |
712 |
|
|
|
713 |
mmeineke |
558 |
// 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 |
tim |
725 |
|
723 |
mmeineke |
558 |
rot[2][0] = 0.0; |
724 |
|
|
rot[2][1] = 0.0; |
725 |
|
|
rot[2][2] = 1.0; |
726 |
tim |
725 |
|
727 |
mmeineke |
558 |
// use a small angle aproximation for sin and cosine |
728 |
|
|
|
729 |
tim |
725 |
angleSqr = angle * angle; |
730 |
mmeineke |
558 |
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 |
tim |
725 |
|
743 |
mmeineke |
558 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
744 |
tim |
725 |
|
745 |
|
|
for (i = 0; i < 3; i++){ |
746 |
mmeineke |
558 |
ji[i] = 0.0; |
747 |
tim |
725 |
for (k = 0; k < 3; k++){ |
748 |
mmeineke |
558 |
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 |
tim |
725 |
for (i = 0; i < 3; i++){ |
761 |
|
|
for (j = 0; j < 3; j++){ |
762 |
gezelter |
600 |
A[j][i] = 0.0; |
763 |
tim |
725 |
for (k = 0; k < 3; k++){ |
764 |
|
|
A[j][i] += tempA[i][k] * rot[j][k]; |
765 |
mmeineke |
558 |
} |
766 |
|
|
} |
767 |
|
|
} |
768 |
|
|
} |
769 |
tim |
677 |
|
770 |
tim |
725 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
771 |
|
|
myFF->doForces(calcPot, calcStress); |
772 |
tim |
677 |
} |
773 |
|
|
|
774 |
|
|
template<typename T> void Integrator<T>::thermalize(){ |
775 |
tim |
725 |
tStats->velocitize(); |
776 |
tim |
677 |
} |
777 |
tim |
763 |
|
778 |
|
|
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
779 |
|
|
return tStats->getTotalE(); |
780 |
mmeineke |
768 |
} |