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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 "simError.h" |
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Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
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Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
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|
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info = theInfo; |
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myFF = the_ff; |
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nAtoms = info->n_atoms; |
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std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
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|
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// check for constraints |
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|
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constrainedA = NULL; |
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constrainedDsqr = NULL; |
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moving = NULL; |
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moved = NULL; |
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prePos = NULL; |
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oldPos = NULL; |
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|
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nConstrained = 0; |
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|
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delete[] constrainedDsqr; |
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delete[] moving; |
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delete[] moved; |
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delete[] prePos; |
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k |
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delete[] oldPos; |
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} |
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} |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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std::cerr << "Is the folowing bond constrained \n"; |
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theArray[j]->printMe(); |
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|
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if(constrained){ |
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std::cerr << "Yes\n"; |
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|
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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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|
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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else std::cerr << "No.\n"; |
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} |
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theArray = (SRI**) molecules[i].getMyBends(); |
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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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} |
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moving = new int[nAtoms]; |
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moved = new int[nAtoms]; |
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prePos = new double[nAtoms*3]; |
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oldPos = new double[nAtoms*3]; |
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} |
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delete[] temp_con; |
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void Integrator::integrate( void ){ |
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int i, j; // loop counters |
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double kE = 0.0; // the kinetic energy |
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double rot_kE; |
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double trans_kE; |
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int tl; // the time loop conter |
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double dt2; // half the dt |
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double vx, vy, vz; // the velocities |
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double vx2, vy2, vz2; // the square of the velocities |
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double rx, ry, rz; // the postitions |
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|
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double ji[3]; // the body frame angular momentum |
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double jx2, jy2, jz2; // the square of the angular momentums |
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double Tb[3]; // torque in the body frame |
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double angle; // the angle through which to rotate the rotation matrix |
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double A[3][3]; // the rotation matrix |
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double press[9]; |
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|
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double dt = info->dt; |
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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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int calcPot, calcStress; |
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int isError; |
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|
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tStats = new Thermo( info ); |
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e_out = new StatWriter( info ); |
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dump_out = new DumpWriter( info ); |
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statOut = new StatWriter( info ); |
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dumpOut = new DumpWriter( info ); |
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|
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Atom** atoms = info->atoms; |
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atoms = info->atoms; |
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DirectionalAtom* dAtom; |
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|
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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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tStats->velocitize(); |
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} |
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dump_out->writeDump( 0.0 ); |
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e_out->writeStat( 0.0 ); |
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dumpOut->writeDump( 0.0 ); |
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statOut->writeStat( 0.0 ); |
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calcPot = 0; |
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calcStress = 0; |
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currStatus = statusTime; |
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currTime = 0.0;; |
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|
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|
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readyCheck(); |
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|
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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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|
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|
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pos = Atom::getPosArray(); |
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vel = Atom::getVelArray(); |
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frc = Atom::getFrcArray(); |
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|
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while( currTime < runTime ){ |
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|
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if( (currTime+dt) >= currStatus ){ |
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calcPot = 1; |
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calcStress = 1; |
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} |
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|
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std::cerr << currTime << "\n"; |
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|
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integrateStep( calcPot, calcStress ); |
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currTime += dt; |
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} |
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if( currTime >= currSample ){ |
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dump_out->writeDump( currTime ); |
249 |
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dumpOut->writeDump( currTime ); |
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currSample += sampleTime; |
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} |
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if( currTime >= currStatus ){ |
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e_out->writeStat( time * dt ); |
254 |
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statOut->writeStat( currTime ); |
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calcPot = 0; |
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calcStress = 0; |
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currStatus += statusTime; |
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} |
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, |
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"successfully took a time step." ); |
263 |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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} |
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< |
dump_out->writeFinal(); |
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> |
dumpOut->writeFinal(currTime); |
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|
270 |
< |
delete dump_out; |
271 |
< |
delete e_out; |
270 |
> |
delete dumpOut; |
271 |
> |
delete statOut; |
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} |
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void Integrator::integrateStep( int calcPot, int calcStress ){ |
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|
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// Position full step, and velocity half step |
279 |
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|
280 |
< |
//preMove(); |
280 |
> |
preMove(); |
281 |
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moveA(); |
282 |
< |
if( nConstrained ) constrainA(); |
282 |
> |
//if( nConstrained ) constrainA(); |
283 |
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|
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// calc forces |
285 |
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|
300 |
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DirectionalAtom* dAtom; |
301 |
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double Tb[3]; |
302 |
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double ji[3]; |
303 |
+ |
double angle; |
304 |
+ |
double A[3][3], At[3][3]; |
305 |
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|
306 |
+ |
|
307 |
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for( i=0; i<nAtoms; i++ ){ |
308 |
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atomIndex = i * 3; |
309 |
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aMatIndex = i * 9; |
310 |
< |
|
310 |
> |
|
311 |
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// velocity half step |
312 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
313 |
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vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
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315 |
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|
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// position whole step |
317 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
318 |
< |
pos[j] += dt * vel[j]; |
317 |
> |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
318 |
> |
|
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295 |
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|
320 |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
326 |
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Tb[0] = dAtom->getTx(); |
327 |
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Tb[1] = dAtom->getTy(); |
328 |
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Tb[2] = dAtom->getTz(); |
329 |
< |
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329 |
> |
|
330 |
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dAtom->lab2Body( Tb ); |
331 |
< |
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331 |
> |
|
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// get the angular momentum, and propagate a half step |
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ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
343 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
344 |
< |
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343 |
> |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
344 |
> |
|
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// rotate about the y-axis |
346 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
347 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
347 |
> |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
348 |
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|
349 |
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// rotate about the z-axis |
350 |
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angle = dt * ji[2] / dAtom->getIzz(); |
351 |
< |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
351 |
> |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
352 |
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|
353 |
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// rotate about the y-axis |
354 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
355 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
355 |
> |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
356 |
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|
357 |
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// rotate about the x-axis |
358 |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
359 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
359 |
> |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
360 |
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|
361 |
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dAtom->setJx( ji[0] ); |
362 |
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dAtom->setJy( ji[1] ); |
363 |
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dAtom->setJz( ji[2] ); |
364 |
+ |
|
365 |
+ |
std::cerr << "Amat[" << i << "]\n"; |
366 |
+ |
info->printMat9( &Amat[aMatIndex] ); |
367 |
+ |
|
368 |
+ |
std::cerr << "ji[" << i << "]\t" |
369 |
+ |
<< ji[0] << "\t" |
370 |
+ |
<< ji[1] << "\t" |
371 |
+ |
<< ji[2] << "\n"; |
372 |
+ |
|
373 |
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} |
374 |
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|
375 |
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} |
378 |
|
|
379 |
|
void Integrator::moveB( void ){ |
380 |
|
int i,j,k; |
381 |
< |
int atomIndex; |
381 |
> |
int atomIndex, aMatIndex; |
382 |
|
DirectionalAtom* dAtom; |
383 |
|
double Tb[3]; |
384 |
|
double ji[3]; |
385 |
|
|
386 |
|
for( i=0; i<nAtoms; i++ ){ |
387 |
|
atomIndex = i * 3; |
388 |
+ |
aMatIndex = i * 9; |
389 |
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|
390 |
|
// velocity half step |
391 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
392 |
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vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
393 |
|
|
394 |
+ |
|
395 |
|
if( atoms[i]->isDirectional() ){ |
396 |
|
|
397 |
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dAtom = (DirectionalAtom *)atoms[i]; |
402 |
|
Tb[1] = dAtom->getTy(); |
403 |
|
Tb[2] = dAtom->getTz(); |
404 |
|
|
405 |
+ |
std::cerr << "TrqB[" << i << "]\t" |
406 |
+ |
<< Tb[0] << "\t" |
407 |
+ |
<< Tb[1] << "\t" |
408 |
+ |
<< Tb[2] << "\n"; |
409 |
+ |
|
410 |
|
dAtom->lab2Body( Tb ); |
411 |
|
|
412 |
|
// get the angular momentum, and complete the angular momentum |
416 |
|
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
417 |
|
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
418 |
|
|
379 |
– |
jx2 = ji[0] * ji[0]; |
380 |
– |
jy2 = ji[1] * ji[1]; |
381 |
– |
jz2 = ji[2] * ji[2]; |
382 |
– |
|
419 |
|
dAtom->setJx( ji[0] ); |
420 |
|
dAtom->setJy( ji[1] ); |
421 |
|
dAtom->setJz( ji[2] ); |
422 |
+ |
|
423 |
+ |
|
424 |
+ |
std::cerr << "Amat[" << i << "]\n"; |
425 |
+ |
info->printMat9( &Amat[aMatIndex] ); |
426 |
+ |
|
427 |
+ |
std::cerr << "ji[" << i << "]\t" |
428 |
+ |
<< ji[0] << "\t" |
429 |
+ |
<< ji[1] << "\t" |
430 |
+ |
<< ji[2] << "\n"; |
431 |
|
} |
432 |
|
} |
433 |
|
|
437 |
|
int i; |
438 |
|
|
439 |
|
if( nConstrained ){ |
440 |
< |
if( oldAtoms != nAtoms ){ |
396 |
< |
|
397 |
< |
// save oldAtoms to check for lode balanceing later on. |
398 |
< |
|
399 |
< |
oldAtoms = nAtoms; |
400 |
< |
|
401 |
< |
delete[] moving; |
402 |
< |
delete[] moved; |
403 |
< |
delete[] oldPos; |
404 |
< |
|
405 |
< |
moving = new int[nAtoms]; |
406 |
< |
moved = new int[nAtoms]; |
407 |
< |
|
408 |
< |
oldPos = new double[nAtoms*3]; |
409 |
< |
} |
410 |
< |
|
440 |
> |
|
441 |
|
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
442 |
|
} |
443 |
|
} |
446 |
|
|
447 |
|
int i,j,k; |
448 |
|
int done; |
449 |
< |
double pxab, pyab, pzab; |
450 |
< |
double rxab, ryab, rzab; |
451 |
< |
int a, b; |
449 |
> |
double pab[3]; |
450 |
> |
double rab[3]; |
451 |
> |
int a, b, ax, ay, az, bx, by, bz; |
452 |
|
double rma, rmb; |
453 |
|
double dx, dy, dz; |
454 |
+ |
double rpab; |
455 |
|
double rabsq, pabsq, rpabsq; |
456 |
|
double diffsq; |
457 |
|
double gab; |
458 |
|
int iteration; |
459 |
|
|
429 |
– |
|
430 |
– |
|
460 |
|
for( i=0; i<nAtoms; i++){ |
461 |
|
|
462 |
|
moving[i] = 0; |
463 |
|
moved[i] = 1; |
464 |
|
} |
465 |
< |
|
437 |
< |
|
465 |
> |
|
466 |
|
iteration = 0; |
467 |
|
done = 0; |
468 |
|
while( !done && (iteration < maxIteration )){ |
472 |
|
|
473 |
|
a = constrainedA[i]; |
474 |
|
b = constrainedB[i]; |
475 |
< |
|
475 |
> |
|
476 |
> |
ax = (a*3) + 0; |
477 |
> |
ay = (a*3) + 1; |
478 |
> |
az = (a*3) + 2; |
479 |
> |
|
480 |
> |
bx = (b*3) + 0; |
481 |
> |
by = (b*3) + 1; |
482 |
> |
bz = (b*3) + 2; |
483 |
> |
|
484 |
|
if( moved[a] || moved[b] ){ |
485 |
|
|
486 |
< |
pxab = pos[3*a+0] - pos[3*b+0]; |
487 |
< |
pyab = pos[3*a+1] - pos[3*b+1]; |
488 |
< |
pzab = pos[3*a+2] - pos[3*b+2]; |
486 |
> |
pab[0] = pos[ax] - pos[bx]; |
487 |
> |
pab[1] = pos[ay] - pos[by]; |
488 |
> |
pab[2] = pos[az] - pos[bz]; |
489 |
|
|
490 |
< |
//periodic boundary condition |
455 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
456 |
< |
* int(pxab / info->box_x + 0.5); |
457 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
458 |
< |
* int(pyab / info->box_y + 0.5); |
459 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
460 |
< |
* int(pzab / info->box_z + 0.5); |
461 |
< |
|
462 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
463 |
< |
rabsq = constraintedDsqr[i]; |
464 |
< |
diffsq = pabsq - rabsq; |
490 |
> |
//periodic boundary condition |
491 |
|
|
492 |
+ |
info->wrapVector( pab ); |
493 |
+ |
|
494 |
+ |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
495 |
+ |
|
496 |
+ |
rabsq = constrainedDsqr[i]; |
497 |
+ |
diffsq = rabsq - pabsq; |
498 |
+ |
|
499 |
|
// the original rattle code from alan tidesley |
500 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
501 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
502 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
503 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
471 |
< |
|
472 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
473 |
< |
* int(rxab / info->box_x + 0.5); |
474 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
475 |
< |
* int(ryab / info->box_y + 0.5); |
476 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
477 |
< |
* int(rzab / info->box_z + 0.5); |
500 |
> |
if (fabs(diffsq) > (tol*rabsq*2)) { |
501 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
502 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
503 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
504 |
|
|
505 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
505 |
> |
info->wrapVector( rab ); |
506 |
> |
|
507 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
508 |
> |
|
509 |
|
rpabsq = rpab * rpab; |
510 |
|
|
511 |
|
|
512 |
|
if (rpabsq < (rabsq * -diffsq)){ |
513 |
+ |
|
514 |
|
#ifdef IS_MPI |
515 |
|
a = atoms[a]->getGlobalIndex(); |
516 |
|
b = atoms[b]->getGlobalIndex(); |
517 |
|
#endif //is_mpi |
518 |
|
sprintf( painCave.errMsg, |
519 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
519 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", |
520 |
|
a, b ); |
521 |
|
painCave.isFatal = 1; |
522 |
|
simError(); |
524 |
|
|
525 |
|
rma = 1.0 / atoms[a]->getMass(); |
526 |
|
rmb = 1.0 / atoms[b]->getMass(); |
527 |
< |
|
527 |
> |
|
528 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
499 |
– |
dx = rxab * gab; |
500 |
– |
dy = ryab * gab; |
501 |
– |
dz = rzab * gab; |
529 |
|
|
530 |
< |
pos[3*a+0] += rma * dx; |
531 |
< |
pos[3*a+1] += rma * dy; |
532 |
< |
pos[3*a+2] += rma * dz; |
530 |
> |
dx = rab[0] * gab; |
531 |
> |
dy = rab[1] * gab; |
532 |
> |
dz = rab[2] * gab; |
533 |
|
|
534 |
< |
pos[3*b+0] -= rmb * dx; |
535 |
< |
pos[3*b+1] -= rmb * dy; |
536 |
< |
pos[3*b+2] -= rmb * dz; |
534 |
> |
pos[ax] += rma * dx; |
535 |
> |
pos[ay] += rma * dy; |
536 |
> |
pos[az] += rma * dz; |
537 |
|
|
538 |
+ |
pos[bx] -= rmb * dx; |
539 |
+ |
pos[by] -= rmb * dy; |
540 |
+ |
pos[bz] -= rmb * dz; |
541 |
+ |
|
542 |
|
dx = dx / dt; |
543 |
|
dy = dy / dt; |
544 |
|
dz = dz / dt; |
545 |
|
|
546 |
< |
vel[3*a+0] += rma * dx; |
547 |
< |
vel[3*a+1] += rma * dy; |
548 |
< |
vel[3*a+2] += rma * dz; |
546 |
> |
vel[ax] += rma * dx; |
547 |
> |
vel[ay] += rma * dy; |
548 |
> |
vel[az] += rma * dz; |
549 |
|
|
550 |
< |
vel[3*b+0] -= rmb * dx; |
551 |
< |
vel[3*b+1] -= rmb * dy; |
552 |
< |
vel[3*b+2] -= rmb * dz; |
550 |
> |
vel[bx] -= rmb * dx; |
551 |
> |
vel[by] -= rmb * dy; |
552 |
> |
vel[bz] -= rmb * dz; |
553 |
|
|
554 |
|
moving[a] = 1; |
555 |
|
moving[b] = 1; |
569 |
|
|
570 |
|
if( !done ){ |
571 |
|
|
572 |
< |
sprintf( painCae.errMsg, |
572 |
> |
sprintf( painCave.errMsg, |
573 |
|
"Constraint failure in constrainA, too many iterations: %d\n", |
574 |
< |
iterations ); |
574 |
> |
iteration ); |
575 |
|
painCave.isFatal = 1; |
576 |
|
simError(); |
577 |
|
} |
583 |
|
int i,j,k; |
584 |
|
int done; |
585 |
|
double vxab, vyab, vzab; |
586 |
< |
double rxab, ryab, rzab; |
587 |
< |
int a, b; |
586 |
> |
double rab[3]; |
587 |
> |
int a, b, ax, ay, az, bx, by, bz; |
588 |
|
double rma, rmb; |
589 |
|
double dx, dy, dz; |
590 |
|
double rabsq, pabsq, rvab; |
592 |
|
double gab; |
593 |
|
int iteration; |
594 |
|
|
595 |
< |
for(i=0; i<nAtom; i++){ |
595 |
> |
for(i=0; i<nAtoms; i++){ |
596 |
|
moving[i] = 0; |
597 |
|
moved[i] = 1; |
598 |
|
} |
599 |
|
|
600 |
|
done = 0; |
601 |
+ |
iteration = 0; |
602 |
|
while( !done && (iteration < maxIteration ) ){ |
603 |
|
|
604 |
+ |
done = 1; |
605 |
+ |
|
606 |
|
for(i=0; i<nConstrained; i++){ |
607 |
|
|
608 |
|
a = constrainedA[i]; |
609 |
|
b = constrainedB[i]; |
610 |
|
|
611 |
+ |
ax = (a*3) + 0; |
612 |
+ |
ay = (a*3) + 1; |
613 |
+ |
az = (a*3) + 2; |
614 |
+ |
|
615 |
+ |
bx = (b*3) + 0; |
616 |
+ |
by = (b*3) + 1; |
617 |
+ |
bz = (b*3) + 2; |
618 |
+ |
|
619 |
|
if( moved[a] || moved[b] ){ |
620 |
|
|
621 |
< |
vxab = vel[3*a+0] - vel[3*b+0]; |
622 |
< |
vyab = vel[3*a+1] - vel[3*b+1]; |
623 |
< |
vzab = vel[3*a+2] - vel[3*b+2]; |
621 |
> |
vxab = vel[ax] - vel[bx]; |
622 |
> |
vyab = vel[ay] - vel[by]; |
623 |
> |
vzab = vel[az] - vel[bz]; |
624 |
|
|
625 |
< |
rxab = pos[3*a+0] - pos[3*b+0];q |
626 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
627 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
625 |
> |
rab[0] = pos[ax] - pos[bx]; |
626 |
> |
rab[1] = pos[ay] - pos[by]; |
627 |
> |
rab[2] = pos[az] - pos[bz]; |
628 |
|
|
629 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
630 |
< |
* int(rxab / info->box_x + 0.5); |
589 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
590 |
< |
* int(ryab / info->box_y + 0.5); |
591 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
592 |
< |
* int(rzab / info->box_z + 0.5); |
593 |
< |
|
629 |
> |
info->wrapVector( rab ); |
630 |
> |
|
631 |
|
rma = 1.0 / atoms[a]->getMass(); |
632 |
|
rmb = 1.0 / atoms[b]->getMass(); |
633 |
|
|
634 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
634 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
635 |
|
|
636 |
< |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
636 |
> |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
637 |
|
|
638 |
|
if (fabs(gab) > tol) { |
639 |
|
|
640 |
< |
dx = rxab * gab; |
641 |
< |
dy = ryab * gab; |
642 |
< |
dz = rzab * gab; |
640 |
> |
dx = rab[0] * gab; |
641 |
> |
dy = rab[1] * gab; |
642 |
> |
dz = rab[2] * gab; |
643 |
|
|
644 |
< |
vel[3*a+0] += rma * dx; |
645 |
< |
vel[3*a+1] += rma * dy; |
646 |
< |
vel[3*a+2] += rma * dz; |
644 |
> |
vel[ax] += rma * dx; |
645 |
> |
vel[ay] += rma * dy; |
646 |
> |
vel[az] += rma * dz; |
647 |
|
|
648 |
< |
vel[3*b+0] -= rmb * dx; |
649 |
< |
vel[3*b+1] -= rmb * dy; |
650 |
< |
vel[3*b+2] -= rmb * dz; |
648 |
> |
vel[bx] -= rmb * dx; |
649 |
> |
vel[by] -= rmb * dy; |
650 |
> |
vel[bz] -= rmb * dz; |
651 |
|
|
652 |
|
moving[a] = 1; |
653 |
|
moving[b] = 1; |
667 |
|
if( !done ){ |
668 |
|
|
669 |
|
|
670 |
< |
sprintf( painCae.errMsg, |
670 |
> |
sprintf( painCave.errMsg, |
671 |
|
"Constraint failure in constrainB, too many iterations: %d\n", |
672 |
< |
iterations ); |
672 |
> |
iteration ); |
673 |
|
painCave.isFatal = 1; |
674 |
|
simError(); |
675 |
|
} |
683 |
|
|
684 |
|
|
685 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
686 |
< |
double A[3][3] ){ |
686 |
> |
double A[9] ){ |
687 |
|
|
688 |
|
int i,j,k; |
689 |
|
double sinAngle; |
695 |
|
double tempA[3][3]; |
696 |
|
double tempJ[3]; |
697 |
|
|
698 |
+ |
|
699 |
|
// initialize the tempA |
700 |
|
|
701 |
|
for(i=0; i<3; i++){ |
702 |
|
for(j=0; j<3; j++){ |
703 |
< |
tempA[j][i] = A[i][j]; |
703 |
> |
tempA[j][i] = A[3*i+j]; |
704 |
|
} |
705 |
|
} |
706 |
|
|
751 |
|
// A[][] = A[][] * transpose(rot[][]) |
752 |
|
|
753 |
|
|
754 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
754 |
> |
// NOte for as yet unknown reason, we are performing the |
755 |
|
// calculation as: |
756 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
757 |
|
|
758 |
|
for(i=0; i<3; i++){ |
759 |
|
for(j=0; j<3; j++){ |
760 |
< |
A[j][i] = 0.0; |
760 |
> |
A[3*j+i] = 0.0; |
761 |
|
for(k=0; k<3; k++){ |
762 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
762 |
> |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
763 |
|
} |
764 |
|
} |
765 |
|
} |