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tim |
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#include <iostream>
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#include <stdlib.h>
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#include <math.h>
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#ifdef IS_MPI
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#include "brains/mpiSimulation.hpp"
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#include <unistd.h>
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#endif //is_mpi
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#ifdef PROFILE
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#include "profiling/mdProfile.hpp"
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#endif // profile
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#include "integrators/Integrator.hpp"
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#include "utils/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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integrableObjects = info->integrableObjects;
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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 balancing 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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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 difference;
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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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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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dt = info->dt;
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dt2 = 0.5 * dt;
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readyCheck();
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// remove center of mass drift velocity (in case we passed in a configuration
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// that was drifting
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tStats->removeCOMdrift();
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// initialize the retraints if necessary
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if (info->useSolidThermInt && !info->useLiquidThermInt) {
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myFF->initRestraints();
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}
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// initialize the forces before the first step
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calcForce(1, 1);
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//execute constraint algorithm to make sure at the very beginning the system is constrained
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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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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 && !stopIntegrator()){
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difference = info->getTime() + dt - currStatus;
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if (difference > 0 || fabs(difference) < 1e-4 ){
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calcPot = 1;
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calcStress = 1;
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}
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#ifdef PROFILE
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startProfile( pro1 );
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#endif
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integrateStep(calcPot, calcStress);
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#ifdef PROFILE
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endProfile( pro1 );
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startProfile( pro2 );
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#endif // profile
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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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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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#ifdef PROFILE
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endProfile( pro2 );
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#endif //profile
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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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dumpOut->writeFinal(info->getTime());
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// dump out a file containing the omega values for the final configuration
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if (info->useSolidThermInt && !info->useLiquidThermInt)
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myFF->dumpzAngle();
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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,
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int calcStress){
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// Position full step, and velocity half step
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#ifdef PROFILE
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startProfile(pro3);
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#endif //profile
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//save old state (position, velocity etc)
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preMove();
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#ifdef PROFILE
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endProfile(pro3);
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startProfile(pro4);
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#endif // profile
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moveA();
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#ifdef PROFILE
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endProfile(pro4);
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startProfile(pro5);
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#endif//profile
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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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#ifdef PROFILE
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endProfile( pro5 );
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startProfile( pro6 );
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#endif //profile
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// finish the velocity half step
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moveB();
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#ifdef PROFILE
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endProfile(pro6);
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#endif // profile
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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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}
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352 |
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353 |
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354 |
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template<typename T> void Integrator<T>::moveA(void){
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size_t i, j;
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DirectionalAtom* dAtom;
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357 |
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Vector3d Tb;
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358 |
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Vector3d ji;
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359 |
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Vector3d vel;
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360 |
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Vector3d pos;
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361 |
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Vector3d frc;
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362 |
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double mass;
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double omega;
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364 |
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365 |
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for (i = 0; i < integrableObjects.size() ; i++){
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vel = integrableObjects[i]->getVel();
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pos = integrableObjects[i]->getPos();
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integrableObjects[i]->getFrc(frc);
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mass = integrableObjects[i]->getMass();
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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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378 |
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integrableObjects[i]->setVel(vel);
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integrableObjects[i]->setPos(pos);
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381 |
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382 |
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if (integrableObjects[i]->isDirectional()){
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384 |
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// get and convert the torque to body frame
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385 |
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Tb = integrableObjects[i]->getTrq();
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integrableObjects[i]->lab2Body(Tb);
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389 |
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// get the angular momentum, and propagate a half step
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390 |
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ji = integrableObjects[i]->getJ();
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392 |
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393 |
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for (j = 0; j < 3; j++)
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ji[j] += (dt2 * Tb[j]) * eConvert;
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395 |
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396 |
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this->rotationPropagation( integrableObjects[i], ji );
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397 |
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398 |
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integrableObjects[i]->setJ(ji);
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399 |
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}
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400 |
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}
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401 |
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|
402 |
|
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if(nConstrained)
|
403 |
|
|
constrainA();
|
404 |
|
|
}
|
405 |
|
|
|
406 |
|
|
|
407 |
|
|
template<typename T> void Integrator<T>::moveB(void){
|
408 |
|
|
int i, j;
|
409 |
|
|
double Tb[3], ji[3];
|
410 |
|
|
double vel[3], frc[3];
|
411 |
|
|
double mass;
|
412 |
|
|
|
413 |
|
|
for (i = 0; i < integrableObjects.size(); i++){
|
414 |
|
|
vel = integrableObjects[i]->getVel();
|
415 |
|
|
integrableObjects[i]->getFrc(frc);
|
416 |
|
|
|
417 |
|
|
mass = integrableObjects[i]->getMass();
|
418 |
|
|
|
419 |
|
|
// velocity half step
|
420 |
|
|
for (j = 0; j < 3; j++)
|
421 |
|
|
vel[j] += (dt2 * frc[j] / mass) * eConvert;
|
422 |
|
|
|
423 |
|
|
integrableObjects[i]->setVel(vel);
|
424 |
|
|
|
425 |
|
|
if (integrableObjects[i]->isDirectional()){
|
426 |
|
|
|
427 |
|
|
// get and convert the torque to body frame
|
428 |
|
|
|
429 |
|
|
Tb = integrableObjects[i]->getTrq();
|
430 |
|
|
integrableObjects[i]->lab2Body(Tb);
|
431 |
|
|
|
432 |
|
|
// get the angular momentum, and propagate a half step
|
433 |
|
|
|
434 |
|
|
ji = integrableObjects[i]->getJ();
|
435 |
|
|
|
436 |
|
|
for (j = 0; j < 3; j++)
|
437 |
|
|
ji[j] += (dt2 * Tb[j]) * eConvert;
|
438 |
|
|
|
439 |
|
|
|
440 |
|
|
integrableObjects[i]->setJ(ji);
|
441 |
|
|
}
|
442 |
|
|
}
|
443 |
|
|
|
444 |
|
|
if(nConstrained)
|
445 |
|
|
constrainB();
|
446 |
|
|
}
|
447 |
|
|
|
448 |
|
|
|
449 |
|
|
template<typename T> void Integrator<T>::preMove(void){
|
450 |
|
|
int i, j;
|
451 |
|
|
double pos[3];
|
452 |
|
|
|
453 |
|
|
if (nConstrained){
|
454 |
|
|
for (i = 0; i < nAtoms; i++){
|
455 |
|
|
pos = atoms[i]->getPos();
|
456 |
|
|
|
457 |
|
|
for (j = 0; j < 3; j++){
|
458 |
|
|
oldPos[3 * i + j] = pos[j];
|
459 |
|
|
}
|
460 |
|
|
}
|
461 |
|
|
}
|
462 |
|
|
}
|
463 |
|
|
|
464 |
|
|
template<typename T> void Integrator<T>::constrainA(){
|
465 |
|
|
int i, j;
|
466 |
|
|
int done;
|
467 |
|
|
double posA[3], posB[3];
|
468 |
|
|
double velA[3], velB[3];
|
469 |
|
|
double pab[3];
|
470 |
|
|
double rab[3];
|
471 |
|
|
int a, b, ax, ay, az, bx, by, bz;
|
472 |
|
|
double rma, rmb;
|
473 |
|
|
double dx, dy, dz;
|
474 |
|
|
double rpab;
|
475 |
|
|
double rabsq, pabsq, rpabsq;
|
476 |
|
|
double diffsq;
|
477 |
|
|
double gab;
|
478 |
|
|
int iteration;
|
479 |
|
|
|
480 |
|
|
for (i = 0; i < nAtoms; i++){
|
481 |
|
|
moving[i] = 0;
|
482 |
|
|
moved[i] = 1;
|
483 |
|
|
}
|
484 |
|
|
|
485 |
|
|
iteration = 0;
|
486 |
|
|
done = 0;
|
487 |
|
|
while (!done && (iteration < maxIteration)){
|
488 |
|
|
done = 1;
|
489 |
|
|
for (i = 0; i < nConstrained; i++){
|
490 |
|
|
a = constrainedA[i];
|
491 |
|
|
b = constrainedB[i];
|
492 |
|
|
|
493 |
|
|
ax = (a * 3) + 0;
|
494 |
|
|
ay = (a * 3) + 1;
|
495 |
|
|
az = (a * 3) + 2;
|
496 |
|
|
|
497 |
|
|
bx = (b * 3) + 0;
|
498 |
|
|
by = (b * 3) + 1;
|
499 |
|
|
bz = (b * 3) + 2;
|
500 |
|
|
|
501 |
|
|
if (moved[a] || moved[b]){
|
502 |
|
|
posA = atoms[a]->getPos();
|
503 |
|
|
posB = atoms[b]->getPos();
|
504 |
|
|
|
505 |
|
|
for (j = 0; j < 3; j++)
|
506 |
|
|
pab[j] = posA[j] - posB[j];
|
507 |
|
|
|
508 |
|
|
//periodic boundary condition
|
509 |
|
|
|
510 |
|
|
info->wrapVector(pab);
|
511 |
|
|
|
512 |
|
|
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
|
513 |
|
|
|
514 |
|
|
rabsq = constrainedDsqr[i];
|
515 |
|
|
diffsq = rabsq - pabsq;
|
516 |
|
|
|
517 |
|
|
// the original rattle code from alan tidesley
|
518 |
|
|
if (fabs(diffsq) > (tol * rabsq * 2)){
|
519 |
|
|
rab[0] = oldPos[ax] - oldPos[bx];
|
520 |
|
|
rab[1] = oldPos[ay] - oldPos[by];
|
521 |
|
|
rab[2] = oldPos[az] - oldPos[bz];
|
522 |
|
|
|
523 |
|
|
info->wrapVector(rab);
|
524 |
|
|
|
525 |
|
|
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
|
526 |
|
|
|
527 |
|
|
rpabsq = rpab * rpab;
|
528 |
|
|
|
529 |
|
|
|
530 |
|
|
if (rpabsq < (rabsq * -diffsq)){
|
531 |
|
|
#ifdef IS_MPI
|
532 |
|
|
a = atoms[a]->getGlobalIndex();
|
533 |
|
|
b = atoms[b]->getGlobalIndex();
|
534 |
|
|
#endif //is_mpi
|
535 |
|
|
sprintf(painCave.errMsg,
|
536 |
|
|
"Constraint failure in constrainA at atom %d and %d.\n", a,
|
537 |
|
|
b);
|
538 |
|
|
painCave.isFatal = 1;
|
539 |
|
|
simError();
|
540 |
|
|
}
|
541 |
|
|
|
542 |
|
|
rma = 1.0 / atoms[a]->getMass();
|
543 |
|
|
rmb = 1.0 / atoms[b]->getMass();
|
544 |
|
|
|
545 |
|
|
gab = diffsq / (2.0 * (rma + rmb) * rpab);
|
546 |
|
|
|
547 |
|
|
dx = rab[0] * gab;
|
548 |
|
|
dy = rab[1] * gab;
|
549 |
|
|
dz = rab[2] * gab;
|
550 |
|
|
|
551 |
|
|
posA[0] += rma * dx;
|
552 |
|
|
posA[1] += rma * dy;
|
553 |
|
|
posA[2] += rma * dz;
|
554 |
|
|
|
555 |
|
|
atoms[a]->setPos(posA);
|
556 |
|
|
|
557 |
|
|
posB[0] -= rmb * dx;
|
558 |
|
|
posB[1] -= rmb * dy;
|
559 |
|
|
posB[2] -= rmb * dz;
|
560 |
|
|
|
561 |
|
|
atoms[b]->setPos(posB);
|
562 |
|
|
|
563 |
|
|
dx = dx / dt;
|
564 |
|
|
dy = dy / dt;
|
565 |
|
|
dz = dz / dt;
|
566 |
|
|
|
567 |
|
|
velA = atoms[a]->getVel();
|
568 |
|
|
|
569 |
|
|
velA[0] += rma * dx;
|
570 |
|
|
velA[1] += rma * dy;
|
571 |
|
|
velA[2] += rma * dz;
|
572 |
|
|
|
573 |
|
|
atoms[a]->setVel(velA);
|
574 |
|
|
|
575 |
|
|
velB = atoms[b]->getVel();
|
576 |
|
|
|
577 |
|
|
velB[0] -= rmb * dx;
|
578 |
|
|
velB[1] -= rmb * dy;
|
579 |
|
|
velB[2] -= rmb * dz;
|
580 |
|
|
|
581 |
|
|
atoms[b]->setVel(velB);
|
582 |
|
|
|
583 |
|
|
moving[a] = 1;
|
584 |
|
|
moving[b] = 1;
|
585 |
|
|
done = 0;
|
586 |
|
|
}
|
587 |
|
|
}
|
588 |
|
|
}
|
589 |
|
|
|
590 |
|
|
for (i = 0; i < nAtoms; i++){
|
591 |
|
|
moved[i] = moving[i];
|
592 |
|
|
moving[i] = 0;
|
593 |
|
|
}
|
594 |
|
|
|
595 |
|
|
iteration++;
|
596 |
|
|
}
|
597 |
|
|
|
598 |
|
|
if (!done){
|
599 |
|
|
sprintf(painCave.errMsg,
|
600 |
|
|
"Constraint failure in constrainA, too many iterations: %d\n",
|
601 |
|
|
iteration);
|
602 |
|
|
painCave.isFatal = 1;
|
603 |
|
|
simError();
|
604 |
|
|
}
|
605 |
|
|
|
606 |
|
|
}
|
607 |
|
|
|
608 |
|
|
template<typename T> void Integrator<T>::constrainB(void){
|
609 |
|
|
int i, j;
|
610 |
|
|
int done;
|
611 |
|
|
double posA[3], posB[3];
|
612 |
|
|
double velA[3], velB[3];
|
613 |
|
|
double vxab, vyab, vzab;
|
614 |
|
|
double rab[3];
|
615 |
|
|
int a, b, ax, ay, az, bx, by, bz;
|
616 |
|
|
double rma, rmb;
|
617 |
|
|
double dx, dy, dz;
|
618 |
|
|
double rvab;
|
619 |
|
|
double gab;
|
620 |
|
|
int iteration;
|
621 |
|
|
|
622 |
|
|
for (i = 0; i < nAtoms; i++){
|
623 |
|
|
moving[i] = 0;
|
624 |
|
|
moved[i] = 1;
|
625 |
|
|
}
|
626 |
|
|
|
627 |
|
|
done = 0;
|
628 |
|
|
iteration = 0;
|
629 |
|
|
while (!done && (iteration < maxIteration)){
|
630 |
|
|
done = 1;
|
631 |
|
|
|
632 |
|
|
for (i = 0; i < nConstrained; i++){
|
633 |
|
|
a = constrainedA[i];
|
634 |
|
|
b = constrainedB[i];
|
635 |
|
|
|
636 |
|
|
ax = (a * 3) + 0;
|
637 |
|
|
ay = (a * 3) + 1;
|
638 |
|
|
az = (a * 3) + 2;
|
639 |
|
|
|
640 |
|
|
bx = (b * 3) + 0;
|
641 |
|
|
by = (b * 3) + 1;
|
642 |
|
|
bz = (b * 3) + 2;
|
643 |
|
|
|
644 |
|
|
if (moved[a] || moved[b]){
|
645 |
|
|
velA = atoms[a]->getVel();
|
646 |
|
|
velB = atoms[b]->getVel();
|
647 |
|
|
|
648 |
|
|
vxab = velA[0] - velB[0];
|
649 |
|
|
vyab = velA[1] - velB[1];
|
650 |
|
|
vzab = velA[2] - velB[2];
|
651 |
|
|
|
652 |
|
|
posA = atoms[a]->getPos();
|
653 |
|
|
posB = atoms[b]->getPos();
|
654 |
|
|
|
655 |
|
|
for (j = 0; j < 3; j++)
|
656 |
|
|
rab[j] = posA[j] - posB[j];
|
657 |
|
|
|
658 |
|
|
info->wrapVector(rab);
|
659 |
|
|
|
660 |
|
|
rma = 1.0 / atoms[a]->getMass();
|
661 |
|
|
rmb = 1.0 / atoms[b]->getMass();
|
662 |
|
|
|
663 |
|
|
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
|
664 |
|
|
|
665 |
|
|
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
|
666 |
|
|
|
667 |
|
|
if (fabs(gab) > tol){
|
668 |
|
|
dx = rab[0] * gab;
|
669 |
|
|
dy = rab[1] * gab;
|
670 |
|
|
dz = rab[2] * gab;
|
671 |
|
|
|
672 |
|
|
velA[0] += rma * dx;
|
673 |
|
|
velA[1] += rma * dy;
|
674 |
|
|
velA[2] += rma * dz;
|
675 |
|
|
|
676 |
|
|
atoms[a]->setVel(velA);
|
677 |
|
|
|
678 |
|
|
velB[0] -= rmb * dx;
|
679 |
|
|
velB[1] -= rmb * dy;
|
680 |
|
|
velB[2] -= rmb * dz;
|
681 |
|
|
|
682 |
|
|
atoms[b]->setVel(velB);
|
683 |
|
|
|
684 |
|
|
moving[a] = 1;
|
685 |
|
|
moving[b] = 1;
|
686 |
|
|
done = 0;
|
687 |
|
|
}
|
688 |
|
|
}
|
689 |
|
|
}
|
690 |
|
|
|
691 |
|
|
for (i = 0; i < nAtoms; i++){
|
692 |
|
|
moved[i] = moving[i];
|
693 |
|
|
moving[i] = 0;
|
694 |
|
|
}
|
695 |
|
|
|
696 |
|
|
iteration++;
|
697 |
|
|
}
|
698 |
|
|
|
699 |
|
|
if (!done){
|
700 |
|
|
sprintf(painCave.errMsg,
|
701 |
|
|
"Constraint failure in constrainB, too many iterations: %d\n",
|
702 |
|
|
iteration);
|
703 |
|
|
painCave.isFatal = 1;
|
704 |
|
|
simError();
|
705 |
|
|
}
|
706 |
|
|
}
|
707 |
|
|
|
708 |
|
|
template<typename T> void Integrator<T>::rotationPropagation
|
709 |
|
|
( StuntDouble* sd, double ji[3] ){
|
710 |
|
|
|
711 |
|
|
double angle;
|
712 |
|
|
double A[3][3], I[3][3];
|
713 |
|
|
int i, j, k;
|
714 |
|
|
|
715 |
|
|
// use the angular velocities to propagate the rotation matrix a
|
716 |
|
|
// full time step
|
717 |
|
|
|
718 |
|
|
sd->getA(A);
|
719 |
|
|
sd->getI(I);
|
720 |
|
|
|
721 |
|
|
if (sd->isLinear()) {
|
722 |
|
|
i = sd->linearAxis();
|
723 |
|
|
j = (i+1)%3;
|
724 |
|
|
k = (i+2)%3;
|
725 |
|
|
|
726 |
|
|
angle = dt2 * ji[j] / I[j][j];
|
727 |
|
|
this->rotate( k, i, angle, ji, A );
|
728 |
|
|
|
729 |
|
|
angle = dt * ji[k] / I[k][k];
|
730 |
|
|
this->rotate( i, j, angle, ji, A);
|
731 |
|
|
|
732 |
|
|
angle = dt2 * ji[j] / I[j][j];
|
733 |
|
|
this->rotate( k, i, angle, ji, A );
|
734 |
|
|
|
735 |
|
|
} else {
|
736 |
|
|
// rotate about the x-axis
|
737 |
|
|
angle = dt2 * ji[0] / I[0][0];
|
738 |
|
|
this->rotate( 1, 2, angle, ji, A );
|
739 |
|
|
|
740 |
|
|
// rotate about the y-axis
|
741 |
|
|
angle = dt2 * ji[1] / I[1][1];
|
742 |
|
|
this->rotate( 2, 0, angle, ji, A );
|
743 |
|
|
|
744 |
|
|
// rotate about the z-axis
|
745 |
|
|
angle = dt * ji[2] / I[2][2];
|
746 |
|
|
sd->addZangle(angle);
|
747 |
|
|
this->rotate( 0, 1, angle, ji, A);
|
748 |
|
|
|
749 |
|
|
// rotate about the y-axis
|
750 |
|
|
angle = dt2 * ji[1] / I[1][1];
|
751 |
|
|
this->rotate( 2, 0, angle, ji, A );
|
752 |
|
|
|
753 |
|
|
// rotate about the x-axis
|
754 |
|
|
angle = dt2 * ji[0] / I[0][0];
|
755 |
|
|
this->rotate( 1, 2, angle, ji, A );
|
756 |
|
|
|
757 |
|
|
}
|
758 |
|
|
sd->setA( A );
|
759 |
|
|
}
|
760 |
|
|
|
761 |
|
|
template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
|
762 |
|
|
double angle, double ji[3],
|
763 |
|
|
double A[3][3]){
|
764 |
|
|
int i, j, k;
|
765 |
|
|
double sinAngle;
|
766 |
|
|
double cosAngle;
|
767 |
|
|
double angleSqr;
|
768 |
|
|
double angleSqrOver4;
|
769 |
|
|
double top, bottom;
|
770 |
|
|
double rot[3][3];
|
771 |
|
|
double tempA[3][3];
|
772 |
|
|
double tempJ[3];
|
773 |
|
|
|
774 |
|
|
// initialize the tempA
|
775 |
|
|
|
776 |
|
|
for (i = 0; i < 3; i++){
|
777 |
|
|
for (j = 0; j < 3; j++){
|
778 |
|
|
tempA[j][i] = A[i][j];
|
779 |
|
|
}
|
780 |
|
|
}
|
781 |
|
|
|
782 |
|
|
// initialize the tempJ
|
783 |
|
|
|
784 |
|
|
for (i = 0; i < 3; i++)
|
785 |
|
|
tempJ[i] = ji[i];
|
786 |
|
|
|
787 |
|
|
// initalize rot as a unit matrix
|
788 |
|
|
|
789 |
|
|
rot[0][0] = 1.0;
|
790 |
|
|
rot[0][1] = 0.0;
|
791 |
|
|
rot[0][2] = 0.0;
|
792 |
|
|
|
793 |
|
|
rot[1][0] = 0.0;
|
794 |
|
|
rot[1][1] = 1.0;
|
795 |
|
|
rot[1][2] = 0.0;
|
796 |
|
|
|
797 |
|
|
rot[2][0] = 0.0;
|
798 |
|
|
rot[2][1] = 0.0;
|
799 |
|
|
rot[2][2] = 1.0;
|
800 |
|
|
|
801 |
|
|
// use a small angle aproximation for sin and cosine
|
802 |
|
|
|
803 |
|
|
angleSqr = angle * angle;
|
804 |
|
|
angleSqrOver4 = angleSqr / 4.0;
|
805 |
|
|
top = 1.0 - angleSqrOver4;
|
806 |
|
|
bottom = 1.0 + angleSqrOver4;
|
807 |
|
|
|
808 |
|
|
cosAngle = top / bottom;
|
809 |
|
|
sinAngle = angle / bottom;
|
810 |
|
|
|
811 |
|
|
rot[axes1][axes1] = cosAngle;
|
812 |
|
|
rot[axes2][axes2] = cosAngle;
|
813 |
|
|
|
814 |
|
|
rot[axes1][axes2] = sinAngle;
|
815 |
|
|
rot[axes2][axes1] = -sinAngle;
|
816 |
|
|
|
817 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[]
|
818 |
|
|
|
819 |
|
|
for (i = 0; i < 3; i++){
|
820 |
|
|
ji[i] = 0.0;
|
821 |
|
|
for (k = 0; k < 3; k++){
|
822 |
|
|
ji[i] += rot[i][k] * tempJ[k];
|
823 |
|
|
}
|
824 |
|
|
}
|
825 |
|
|
|
826 |
|
|
// rotate the Rotation matrix acording to:
|
827 |
|
|
// A[][] = A[][] * transpose(rot[][])
|
828 |
|
|
|
829 |
|
|
|
830 |
|
|
// NOte for as yet unknown reason, we are performing the
|
831 |
|
|
// calculation as:
|
832 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
|
833 |
|
|
|
834 |
|
|
for (i = 0; i < 3; i++){
|
835 |
|
|
for (j = 0; j < 3; j++){
|
836 |
|
|
A[j][i] = 0.0;
|
837 |
|
|
for (k = 0; k < 3; k++){
|
838 |
|
|
A[j][i] += tempA[i][k] * rot[j][k];
|
839 |
|
|
}
|
840 |
|
|
}
|
841 |
|
|
}
|
842 |
|
|
}
|
843 |
|
|
|
844 |
|
|
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
|
845 |
|
|
myFF->doForces(calcPot, calcStress);
|
846 |
|
|
}
|
847 |
|
|
|
848 |
|
|
template<typename T> void Integrator<T>::thermalize(){
|
849 |
|
|
tStats->velocitize();
|
850 |
|
|
}
|
851 |
|
|
|
852 |
|
|
template<typename T> double Integrator<T>::getConservedQuantity(void){
|
853 |
|
|
return tStats->getTotalE();
|
854 |
|
|
}
|
855 |
|
|
template<typename T> string Integrator<T>::getAdditionalParameters(void){
|
856 |
|
|
//By default, return a null string
|
857 |
|
|
//The reason we use string instead of char* is that if we use char*, we will
|
858 |
|
|
//return a pointer point to local variable which might cause problem
|
859 |
|
|
return string();
|
860 |
|
|
}
|