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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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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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} |
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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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|
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|
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if(constrained){ |
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|
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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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nConstrained++; |
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constrained = 0; |
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} |
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} |
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} |
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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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|
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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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double currSample; |
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double currThermal; |
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double currStatus; |
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double currTime; |
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|
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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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|
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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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|
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calcPot = 0; |
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calcStress = 0; |
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currSample = sampleTime; |
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currThermal = thermalTime; |
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currStatus = statusTime; |
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currTime = 0.0;; |
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while( currTime < runTime ){ |
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dumpOut->writeDump( info->currTime ); |
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statOut->writeStat( info->currTime ); |
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if( (currTime+dt) >= currStatus ){ |
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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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while( info->currTime < runTime ){ |
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|
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if( (info->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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integrateStep( calcPot, calcStress ); |
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currTime += dt; |
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info->currTime += dt; |
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info->setTime(info->currTime); |
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|
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if( info->setTemp ){ |
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if( currTime >= currThermal ){ |
223 |
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if( info->currTime >= currThermal ){ |
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tStats->velocitize(); |
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currThermal += thermalTime; |
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} |
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} |
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if( currTime >= currSample ){ |
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dump_out->writeDump( currTime ); |
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if( info->currTime >= currSample ){ |
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dumpOut->writeDump( info->currTime ); |
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currSample += sampleTime; |
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} |
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if( currTime >= currStatus ){ |
235 |
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e_out->writeStat( time * dt ); |
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if( info->currTime >= currStatus ){ |
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statOut->writeStat( info->currTime ); |
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calcPot = 0; |
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calcStress = 0; |
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currStatus += statusTime; |
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} |
247 |
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} |
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|
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dump_out->writeFinal(); |
241 |
> |
#ifdef IS_MPI |
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> |
strcpy( checkPointMsg, |
243 |
> |
"successfully took a time step." ); |
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MPIcheckPoint(); |
245 |
> |
#endif // is_mpi |
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|
247 |
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delete dump_out; |
248 |
< |
delete e_out; |
247 |
> |
} |
248 |
> |
|
249 |
> |
dumpOut->writeFinal(info->currTime); |
250 |
> |
|
251 |
> |
delete dumpOut; |
252 |
> |
delete statOut; |
253 |
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} |
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|
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void Integrator::integrateStep( int calcPot, int calcStress ){ |
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257 |
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|
258 |
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|
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// Position full step, and velocity half step |
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|
261 |
< |
//preMove(); |
261 |
> |
preMove(); |
262 |
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moveA(); |
263 |
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if( nConstrained ) constrainA(); |
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|
265 |
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|
266 |
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#ifdef IS_MPI |
267 |
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strcpy( checkPointMsg, "Succesful moveA\n" ); |
268 |
+ |
MPIcheckPoint(); |
269 |
+ |
#endif // is_mpi |
270 |
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|
271 |
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|
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// calc forces |
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|
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myFF->doForces(calcPot,calcStress); |
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|
276 |
+ |
#ifdef IS_MPI |
277 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
278 |
+ |
MPIcheckPoint(); |
279 |
+ |
#endif // is_mpi |
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|
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|
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// finish the velocity half step |
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moveB(); |
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if( nConstrained ) constrainB(); |
286 |
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286 |
> |
|
287 |
> |
#ifdef IS_MPI |
288 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
289 |
> |
MPIcheckPoint(); |
290 |
> |
#endif // is_mpi |
291 |
> |
|
292 |
> |
|
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} |
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void Integrator::moveA( void ){ |
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|
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int i,j,k; |
278 |
< |
int atomIndex, aMatIndex; |
298 |
> |
int i, j; |
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DirectionalAtom* dAtom; |
300 |
< |
double Tb[3]; |
301 |
< |
double ji[3]; |
300 |
> |
double Tb[3], ji[3]; |
301 |
> |
double A[3][3], I[3][3]; |
302 |
> |
double angle; |
303 |
> |
double vel[3], pos[3], frc[3]; |
304 |
> |
double mass; |
305 |
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|
306 |
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for( i=0; i<nAtoms; i++ ){ |
284 |
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atomIndex = i * 3; |
285 |
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aMatIndex = i * 9; |
286 |
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|
287 |
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// velocity half step |
288 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
289 |
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vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
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|
308 |
< |
// position whole step |
309 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
308 |
> |
atoms[i]->getVel( vel ); |
309 |
> |
atoms[i]->getPos( pos ); |
310 |
> |
atoms[i]->getFrc( frc ); |
311 |
> |
|
312 |
> |
mass = atoms[i]->getMass(); |
313 |
> |
|
314 |
> |
for (j=0; j < 3; j++) { |
315 |
> |
// velocity half step |
316 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
317 |
> |
// position whole step |
318 |
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pos[j] += dt * vel[j]; |
319 |
+ |
} |
320 |
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|
321 |
< |
|
321 |
> |
atoms[i]->setVel( vel ); |
322 |
> |
atoms[i]->setPos( pos ); |
323 |
> |
|
324 |
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if( atoms[i]->isDirectional() ){ |
325 |
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|
326 |
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dAtom = (DirectionalAtom *)atoms[i]; |
327 |
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|
328 |
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// get and convert the torque to body frame |
329 |
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|
330 |
< |
Tb[0] = dAtom->getTx(); |
303 |
< |
Tb[1] = dAtom->getTy(); |
304 |
< |
Tb[2] = dAtom->getTz(); |
305 |
< |
|
330 |
> |
dAtom->getTrq( Tb ); |
331 |
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dAtom->lab2Body( Tb ); |
332 |
< |
|
332 |
> |
|
333 |
|
// get the angular momentum, and propagate a half step |
334 |
+ |
|
335 |
+ |
dAtom->getJ( ji ); |
336 |
+ |
|
337 |
+ |
for (j=0; j < 3; j++) |
338 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
339 |
|
|
310 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
311 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
312 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
313 |
– |
|
340 |
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// use the angular velocities to propagate the rotation matrix a |
341 |
|
// full time step |
342 |
< |
|
342 |
> |
|
343 |
> |
dAtom->getA(A); |
344 |
> |
dAtom->getI(I); |
345 |
> |
|
346 |
|
// rotate about the x-axis |
347 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
348 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
349 |
< |
|
347 |
> |
angle = dt2 * ji[0] / I[0][0]; |
348 |
> |
this->rotate( 1, 2, angle, ji, A ); |
349 |
> |
|
350 |
|
// rotate about the y-axis |
351 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
352 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
351 |
> |
angle = dt2 * ji[1] / I[1][1]; |
352 |
> |
this->rotate( 2, 0, angle, ji, A ); |
353 |
|
|
354 |
|
// rotate about the z-axis |
355 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
356 |
< |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
355 |
> |
angle = dt * ji[2] / I[2][2]; |
356 |
> |
this->rotate( 0, 1, angle, ji, A); |
357 |
|
|
358 |
|
// rotate about the y-axis |
359 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
360 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
359 |
> |
angle = dt2 * ji[1] / I[1][1]; |
360 |
> |
this->rotate( 2, 0, angle, ji, A ); |
361 |
|
|
362 |
|
// rotate about the x-axis |
363 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
364 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
363 |
> |
angle = dt2 * ji[0] / I[0][0]; |
364 |
> |
this->rotate( 1, 2, angle, ji, A ); |
365 |
|
|
366 |
< |
dAtom->setJx( ji[0] ); |
367 |
< |
dAtom->setJy( ji[1] ); |
368 |
< |
dAtom->setJz( ji[2] ); |
369 |
< |
} |
370 |
< |
|
366 |
> |
|
367 |
> |
dAtom->setJ( ji ); |
368 |
> |
dAtom->setA( A ); |
369 |
> |
|
370 |
> |
} |
371 |
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} |
372 |
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} |
373 |
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|
374 |
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|
375 |
|
void Integrator::moveB( void ){ |
376 |
< |
int i,j,k; |
348 |
< |
int atomIndex; |
376 |
> |
int i, j; |
377 |
|
DirectionalAtom* dAtom; |
378 |
< |
double Tb[3]; |
379 |
< |
double ji[3]; |
378 |
> |
double Tb[3], ji[3]; |
379 |
> |
double vel[3], frc[3]; |
380 |
> |
double mass; |
381 |
|
|
382 |
|
for( i=0; i<nAtoms; i++ ){ |
383 |
< |
atomIndex = i * 3; |
383 |
> |
|
384 |
> |
atoms[i]->getVel( vel ); |
385 |
> |
atoms[i]->getFrc( frc ); |
386 |
|
|
387 |
< |
// velocity half step |
357 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
358 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
387 |
> |
mass = atoms[i]->getMass(); |
388 |
|
|
389 |
+ |
// velocity half step |
390 |
+ |
for (j=0; j < 3; j++) |
391 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
392 |
+ |
|
393 |
+ |
atoms[i]->setVel( vel ); |
394 |
+ |
|
395 |
|
if( atoms[i]->isDirectional() ){ |
396 |
< |
|
396 |
> |
|
397 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
398 |
< |
|
399 |
< |
// get and convert the torque to body frame |
400 |
< |
|
401 |
< |
Tb[0] = dAtom->getTx(); |
367 |
< |
Tb[1] = dAtom->getTy(); |
368 |
< |
Tb[2] = dAtom->getTz(); |
369 |
< |
|
398 |
> |
|
399 |
> |
// get and convert the torque to body frame |
400 |
> |
|
401 |
> |
dAtom->getTrq( Tb ); |
402 |
|
dAtom->lab2Body( Tb ); |
403 |
+ |
|
404 |
+ |
// get the angular momentum, and propagate a half step |
405 |
+ |
|
406 |
+ |
dAtom->getJ( ji ); |
407 |
+ |
|
408 |
+ |
for (j=0; j < 3; j++) |
409 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
410 |
|
|
411 |
< |
// get the angular momentum, and complete the angular momentum |
412 |
< |
// half step |
374 |
< |
|
375 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
376 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
377 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
378 |
< |
|
379 |
< |
jx2 = ji[0] * ji[0]; |
380 |
< |
jy2 = ji[1] * ji[1]; |
381 |
< |
jz2 = ji[2] * ji[2]; |
382 |
< |
|
383 |
< |
dAtom->setJx( ji[0] ); |
384 |
< |
dAtom->setJy( ji[1] ); |
385 |
< |
dAtom->setJz( ji[2] ); |
411 |
> |
|
412 |
> |
dAtom->setJ( ji ); |
413 |
|
} |
414 |
|
} |
388 |
– |
|
415 |
|
} |
416 |
|
|
417 |
|
void Integrator::preMove( void ){ |
418 |
< |
int i; |
418 |
> |
int i, j; |
419 |
> |
double pos[3]; |
420 |
|
|
421 |
|
if( nConstrained ){ |
422 |
< |
if( oldAtoms != nAtoms ){ |
423 |
< |
|
424 |
< |
// save oldAtoms to check for lode balanceing later on. |
425 |
< |
|
426 |
< |
oldAtoms = nAtoms; |
427 |
< |
|
428 |
< |
delete[] moving; |
429 |
< |
delete[] moved; |
430 |
< |
delete[] oldPos; |
404 |
< |
|
405 |
< |
moving = new int[nAtoms]; |
406 |
< |
moved = new int[nAtoms]; |
407 |
< |
|
408 |
< |
oldPos = new double[nAtoms*3]; |
422 |
> |
|
423 |
> |
for(i=0; i < nAtoms; i++) { |
424 |
> |
|
425 |
> |
atoms[i]->getPos( pos ); |
426 |
> |
|
427 |
> |
for (j = 0; j < 3; j++) { |
428 |
> |
oldPos[3*i + j] = pos[j]; |
429 |
> |
} |
430 |
> |
|
431 |
|
} |
432 |
< |
|
433 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
412 |
< |
} |
413 |
< |
} |
432 |
> |
} |
433 |
> |
} |
434 |
|
|
435 |
|
void Integrator::constrainA(){ |
436 |
|
|
437 |
|
int i,j,k; |
438 |
|
int done; |
439 |
< |
double pxab, pyab, pzab; |
440 |
< |
double rxab, ryab, rzab; |
441 |
< |
int a, b; |
439 |
> |
double posA[3], posB[3]; |
440 |
> |
double velA[3], velB[3]; |
441 |
> |
double pab[3]; |
442 |
> |
double rab[3]; |
443 |
> |
int a, b, ax, ay, az, bx, by, bz; |
444 |
|
double rma, rmb; |
445 |
|
double dx, dy, dz; |
446 |
+ |
double rpab; |
447 |
|
double rabsq, pabsq, rpabsq; |
448 |
|
double diffsq; |
449 |
|
double gab; |
450 |
|
int iteration; |
451 |
|
|
452 |
< |
|
430 |
< |
|
431 |
< |
for( i=0; i<nAtoms; i++){ |
432 |
< |
|
452 |
> |
for( i=0; i<nAtoms; i++){ |
453 |
|
moving[i] = 0; |
454 |
|
moved[i] = 1; |
455 |
|
} |
456 |
< |
|
437 |
< |
|
456 |
> |
|
457 |
|
iteration = 0; |
458 |
|
done = 0; |
459 |
|
while( !done && (iteration < maxIteration )){ |
463 |
|
|
464 |
|
a = constrainedA[i]; |
465 |
|
b = constrainedB[i]; |
466 |
< |
|
466 |
> |
|
467 |
> |
ax = (a*3) + 0; |
468 |
> |
ay = (a*3) + 1; |
469 |
> |
az = (a*3) + 2; |
470 |
> |
|
471 |
> |
bx = (b*3) + 0; |
472 |
> |
by = (b*3) + 1; |
473 |
> |
bz = (b*3) + 2; |
474 |
> |
|
475 |
|
if( moved[a] || moved[b] ){ |
476 |
< |
|
477 |
< |
pxab = pos[3*a+0] - pos[3*b+0]; |
478 |
< |
pyab = pos[3*a+1] - pos[3*b+1]; |
479 |
< |
pzab = pos[3*a+2] - pos[3*b+2]; |
476 |
> |
|
477 |
> |
atoms[a]->getPos( posA ); |
478 |
> |
atoms[b]->getPos( posB ); |
479 |
> |
|
480 |
> |
for (j = 0; j < 3; j++ ) |
481 |
> |
pab[j] = posA[j] - posB[j]; |
482 |
> |
|
483 |
> |
//periodic boundary condition |
484 |
|
|
485 |
< |
//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; |
485 |
> |
info->wrapVector( pab ); |
486 |
|
|
487 |
+ |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
488 |
+ |
|
489 |
+ |
rabsq = constrainedDsqr[i]; |
490 |
+ |
diffsq = rabsq - pabsq; |
491 |
+ |
|
492 |
|
// the original rattle code from alan tidesley |
493 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
494 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
495 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
496 |
< |
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); |
493 |
> |
if (fabs(diffsq) > (tol*rabsq*2)) { |
494 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
495 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
496 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
497 |
|
|
498 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
498 |
> |
info->wrapVector( rab ); |
499 |
> |
|
500 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
501 |
> |
|
502 |
|
rpabsq = rpab * rpab; |
503 |
|
|
504 |
|
|
505 |
|
if (rpabsq < (rabsq * -diffsq)){ |
506 |
+ |
|
507 |
|
#ifdef IS_MPI |
508 |
|
a = atoms[a]->getGlobalIndex(); |
509 |
|
b = atoms[b]->getGlobalIndex(); |
510 |
|
#endif //is_mpi |
511 |
|
sprintf( painCave.errMsg, |
512 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
512 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", |
513 |
|
a, b ); |
514 |
|
painCave.isFatal = 1; |
515 |
|
simError(); |
517 |
|
|
518 |
|
rma = 1.0 / atoms[a]->getMass(); |
519 |
|
rmb = 1.0 / atoms[b]->getMass(); |
520 |
< |
|
520 |
> |
|
521 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
499 |
– |
dx = rxab * gab; |
500 |
– |
dy = ryab * gab; |
501 |
– |
dz = rzab * gab; |
522 |
|
|
523 |
< |
pos[3*a+0] += rma * dx; |
524 |
< |
pos[3*a+1] += rma * dy; |
525 |
< |
pos[3*a+2] += rma * dz; |
523 |
> |
dx = rab[0] * gab; |
524 |
> |
dy = rab[1] * gab; |
525 |
> |
dz = rab[2] * gab; |
526 |
|
|
527 |
< |
pos[3*b+0] -= rmb * dx; |
528 |
< |
pos[3*b+1] -= rmb * dy; |
529 |
< |
pos[3*b+2] -= rmb * dz; |
527 |
> |
posA[0] += rma * dx; |
528 |
> |
posA[1] += rma * dy; |
529 |
> |
posA[2] += rma * dz; |
530 |
> |
|
531 |
> |
atoms[a]->setPos( posA ); |
532 |
> |
|
533 |
> |
posB[0] -= rmb * dx; |
534 |
> |
posB[1] -= rmb * dy; |
535 |
> |
posB[2] -= rmb * dz; |
536 |
> |
|
537 |
> |
atoms[b]->setPos( posB ); |
538 |
|
|
539 |
|
dx = dx / dt; |
540 |
|
dy = dy / dt; |
541 |
|
dz = dz / dt; |
542 |
|
|
543 |
< |
vel[3*a+0] += rma * dx; |
516 |
< |
vel[3*a+1] += rma * dy; |
517 |
< |
vel[3*a+2] += rma * dz; |
543 |
> |
atoms[a]->getVel( velA ); |
544 |
|
|
545 |
< |
vel[3*b+0] -= rmb * dx; |
546 |
< |
vel[3*b+1] -= rmb * dy; |
547 |
< |
vel[3*b+2] -= rmb * dz; |
545 |
> |
velA[0] += rma * dx; |
546 |
> |
velA[1] += rma * dy; |
547 |
> |
velA[2] += rma * dz; |
548 |
|
|
549 |
+ |
atoms[a]->setVel( velA ); |
550 |
+ |
|
551 |
+ |
atoms[b]->getVel( velB ); |
552 |
+ |
|
553 |
+ |
velB[0] -= rmb * dx; |
554 |
+ |
velB[1] -= rmb * dy; |
555 |
+ |
velB[2] -= rmb * dz; |
556 |
+ |
|
557 |
+ |
atoms[b]->setVel( velB ); |
558 |
+ |
|
559 |
|
moving[a] = 1; |
560 |
|
moving[b] = 1; |
561 |
|
done = 0; |
574 |
|
|
575 |
|
if( !done ){ |
576 |
|
|
577 |
< |
sprintf( painCae.errMsg, |
577 |
> |
sprintf( painCave.errMsg, |
578 |
|
"Constraint failure in constrainA, too many iterations: %d\n", |
579 |
< |
iterations ); |
579 |
> |
iteration ); |
580 |
|
painCave.isFatal = 1; |
581 |
|
simError(); |
582 |
|
} |
587 |
|
|
588 |
|
int i,j,k; |
589 |
|
int done; |
590 |
+ |
double posA[3], posB[3]; |
591 |
+ |
double velA[3], velB[3]; |
592 |
|
double vxab, vyab, vzab; |
593 |
< |
double rxab, ryab, rzab; |
594 |
< |
int a, b; |
593 |
> |
double rab[3]; |
594 |
> |
int a, b, ax, ay, az, bx, by, bz; |
595 |
|
double rma, rmb; |
596 |
|
double dx, dy, dz; |
597 |
|
double rabsq, pabsq, rvab; |
599 |
|
double gab; |
600 |
|
int iteration; |
601 |
|
|
602 |
< |
for(i=0; i<nAtom; i++){ |
602 |
> |
for(i=0; i<nAtoms; i++){ |
603 |
|
moving[i] = 0; |
604 |
|
moved[i] = 1; |
605 |
|
} |
606 |
|
|
607 |
|
done = 0; |
608 |
+ |
iteration = 0; |
609 |
|
while( !done && (iteration < maxIteration ) ){ |
610 |
|
|
611 |
+ |
done = 1; |
612 |
+ |
|
613 |
|
for(i=0; i<nConstrained; i++){ |
614 |
|
|
615 |
|
a = constrainedA[i]; |
616 |
|
b = constrainedB[i]; |
617 |
|
|
618 |
+ |
ax = (a*3) + 0; |
619 |
+ |
ay = (a*3) + 1; |
620 |
+ |
az = (a*3) + 2; |
621 |
+ |
|
622 |
+ |
bx = (b*3) + 0; |
623 |
+ |
by = (b*3) + 1; |
624 |
+ |
bz = (b*3) + 2; |
625 |
+ |
|
626 |
|
if( moved[a] || moved[b] ){ |
578 |
– |
|
579 |
– |
vxab = vel[3*a+0] - vel[3*b+0]; |
580 |
– |
vyab = vel[3*a+1] - vel[3*b+1]; |
581 |
– |
vzab = vel[3*a+2] - vel[3*b+2]; |
627 |
|
|
628 |
< |
rxab = pos[3*a+0] - pos[3*b+0];q |
629 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
630 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
631 |
< |
|
632 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
633 |
< |
* 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); |
628 |
> |
atoms[a]->getVel( velA ); |
629 |
> |
atoms[b]->getVel( velB ); |
630 |
> |
|
631 |
> |
vxab = velA[0] - velB[0]; |
632 |
> |
vyab = velA[1] - velB[1]; |
633 |
> |
vzab = velA[2] - velB[2]; |
634 |
|
|
635 |
+ |
atoms[a]->getPos( posA ); |
636 |
+ |
atoms[b]->getPos( posB ); |
637 |
+ |
|
638 |
+ |
for (j = 0; j < 3; j++) |
639 |
+ |
rab[j] = posA[j] - posB[j]; |
640 |
+ |
|
641 |
+ |
info->wrapVector( rab ); |
642 |
+ |
|
643 |
|
rma = 1.0 / atoms[a]->getMass(); |
644 |
|
rmb = 1.0 / atoms[b]->getMass(); |
645 |
|
|
646 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
646 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
647 |
|
|
648 |
< |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
648 |
> |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
649 |
|
|
650 |
|
if (fabs(gab) > tol) { |
651 |
|
|
652 |
< |
dx = rxab * gab; |
653 |
< |
dy = ryab * gab; |
654 |
< |
dz = rzab * gab; |
655 |
< |
|
656 |
< |
vel[3*a+0] += rma * dx; |
657 |
< |
vel[3*a+1] += rma * dy; |
658 |
< |
vel[3*a+2] += rma * dz; |
652 |
> |
dx = rab[0] * gab; |
653 |
> |
dy = rab[1] * gab; |
654 |
> |
dz = rab[2] * gab; |
655 |
> |
|
656 |
> |
velA[0] += rma * dx; |
657 |
> |
velA[1] += rma * dy; |
658 |
> |
velA[2] += rma * dz; |
659 |
|
|
660 |
< |
vel[3*b+0] -= rmb * dx; |
661 |
< |
vel[3*b+1] -= rmb * dy; |
662 |
< |
vel[3*b+2] -= rmb * dz; |
660 |
> |
atoms[a]->setVel( velA ); |
661 |
> |
|
662 |
> |
velB[0] -= rmb * dx; |
663 |
> |
velB[1] -= rmb * dy; |
664 |
> |
velB[2] -= rmb * dz; |
665 |
> |
|
666 |
> |
atoms[b]->setVel( velB ); |
667 |
|
|
668 |
|
moving[a] = 1; |
669 |
|
moving[b] = 1; |
679 |
|
|
680 |
|
iteration++; |
681 |
|
} |
682 |
< |
|
682 |
> |
|
683 |
|
if( !done ){ |
684 |
|
|
685 |
|
|
686 |
< |
sprintf( painCae.errMsg, |
686 |
> |
sprintf( painCave.errMsg, |
687 |
|
"Constraint failure in constrainB, too many iterations: %d\n", |
688 |
< |
iterations ); |
688 |
> |
iteration ); |
689 |
|
painCave.isFatal = 1; |
690 |
|
simError(); |
691 |
|
} |
692 |
|
|
693 |
|
} |
694 |
|
|
642 |
– |
|
643 |
– |
|
644 |
– |
|
645 |
– |
|
646 |
– |
|
647 |
– |
|
695 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
696 |
|
double A[3][3] ){ |
697 |
|
|
760 |
|
// A[][] = A[][] * transpose(rot[][]) |
761 |
|
|
762 |
|
|
763 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
763 |
> |
// NOte for as yet unknown reason, we are performing the |
764 |
|
// calculation as: |
765 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
766 |
|
|