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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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|
39 |
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nConstrained = 0; |
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|
49 |
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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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delete[] oldPos; |
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} |
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55 |
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} |
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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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|
141 |
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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 |
159 |
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double kE = 0.0; // the kinetic energy |
160 |
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double rot_kE; |
161 |
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double trans_kE; |
162 |
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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 |
166 |
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double vx2, vy2, vz2; // the square of the velocities |
167 |
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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 |
170 |
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double jx2, jy2, jz2; // the square of the angular momentums |
171 |
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double Tb[3]; // torque in the body frame |
172 |
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double angle; // the angle through which to rotate the rotation matrix |
173 |
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double A[3][3]; // the rotation matrix |
174 |
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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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|
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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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|
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calcPot = 0; |
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calcStress = 0; |
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MPIcheckPoint(); |
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#endif // is_mpi |
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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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trq = Atom::getTrqArray(); |
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Amat = Atom::getAmatArray(); |
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|
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while( currTime < runTime ){ |
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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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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 ); |
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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 ); |
246 |
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statOut->writeStat( currTime ); |
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calcPot = 0; |
248 |
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calcStress = 0; |
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currStatus += statusTime; |
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} |
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dump_out->writeFinal(); |
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dumpOut->writeFinal(); |
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262 |
< |
delete dump_out; |
263 |
< |
delete e_out; |
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> |
delete dumpOut; |
263 |
> |
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 |
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|
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//preMove(); |
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preMove(); |
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moveA(); |
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if( nConstrained ) constrainA(); |
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DirectionalAtom* dAtom; |
293 |
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double Tb[3]; |
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double ji[3]; |
295 |
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double angle; |
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298 |
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
302 |
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|
302 |
> |
|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
305 |
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vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
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|
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// position whole step |
308 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
309 |
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pos[j] += dt * vel[j]; |
309 |
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310 |
< |
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308 |
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for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
309 |
> |
|
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
333 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
333 |
> |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
334 |
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|
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// rotate about the y-axis |
336 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
337 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
337 |
> |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
338 |
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|
339 |
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// rotate about the z-axis |
340 |
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angle = dt * ji[2] / dAtom->getIzz(); |
341 |
< |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
341 |
> |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
342 |
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|
343 |
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// rotate about the y-axis |
344 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
345 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
345 |
> |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
346 |
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|
347 |
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// rotate about the x-axis |
348 |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
349 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
349 |
> |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
351 |
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dAtom->setJx( ji[0] ); |
352 |
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dAtom->setJy( ji[1] ); |
390 |
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ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
391 |
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ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
392 |
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394 |
– |
jx2 = ji[0] * ji[0]; |
395 |
– |
jy2 = ji[1] * ji[1]; |
396 |
– |
jz2 = ji[2] * ji[2]; |
397 |
– |
|
393 |
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dAtom->setJx( ji[0] ); |
394 |
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dAtom->setJy( ji[1] ); |
395 |
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dAtom->setJz( ji[2] ); |
402 |
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int i; |
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404 |
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if( nConstrained ){ |
405 |
< |
if( oldAtoms != nAtoms ){ |
411 |
< |
|
412 |
< |
// save oldAtoms to check for lode balanceing later on. |
413 |
< |
|
414 |
< |
oldAtoms = nAtoms; |
415 |
< |
|
416 |
< |
delete[] moving; |
417 |
< |
delete[] moved; |
418 |
< |
delete[] oldPos; |
419 |
< |
|
420 |
< |
moving = new int[nAtoms]; |
421 |
< |
moved = new int[nAtoms]; |
422 |
< |
|
423 |
< |
oldPos = new double[nAtoms*3]; |
424 |
< |
} |
425 |
< |
|
405 |
> |
|
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for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
407 |
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} |
408 |
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} |
413 |
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int done; |
414 |
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double pxab, pyab, pzab; |
415 |
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double rxab, ryab, rzab; |
416 |
< |
int a, b; |
416 |
> |
int a, b, ax, ay, az, bx, by, bz; |
417 |
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double rma, rmb; |
418 |
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double dx, dy, dz; |
419 |
+ |
double rpab; |
420 |
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double rabsq, pabsq, rpabsq; |
421 |
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double diffsq; |
422 |
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double gab; |
429 |
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moving[i] = 0; |
430 |
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moved[i] = 1; |
431 |
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} |
432 |
< |
|
452 |
< |
|
432 |
> |
|
433 |
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iteration = 0; |
434 |
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done = 0; |
435 |
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while( !done && (iteration < maxIteration )){ |
439 |
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|
440 |
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a = constrainedA[i]; |
441 |
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b = constrainedB[i]; |
442 |
< |
|
442 |
> |
|
443 |
> |
ax = (a*3) + 0; |
444 |
> |
ay = (a*3) + 1; |
445 |
> |
az = (a*3) + 2; |
446 |
> |
|
447 |
> |
bx = (b*3) + 0; |
448 |
> |
by = (b*3) + 1; |
449 |
> |
bz = (b*3) + 2; |
450 |
> |
|
451 |
|
if( moved[a] || moved[b] ){ |
452 |
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|
453 |
< |
pxab = pos[3*a+0] - pos[3*b+0]; |
454 |
< |
pyab = pos[3*a+1] - pos[3*b+1]; |
455 |
< |
pzab = pos[3*a+2] - pos[3*b+2]; |
453 |
> |
pxab = pos[ax] - pos[bx]; |
454 |
> |
pyab = pos[ay] - pos[by]; |
455 |
> |
pzab = pos[az] - pos[bz]; |
456 |
|
|
457 |
< |
//periodic boundary condition |
457 |
> |
//periodic boundary condition |
458 |
|
pxab = pxab - info->box_x * copysign(1, pxab) |
459 |
< |
* int(pxab / info->box_x + 0.5); |
459 |
> |
* (int)( fabs(pxab / info->box_x) + 0.5); |
460 |
|
pyab = pyab - info->box_y * copysign(1, pyab) |
461 |
< |
* int(pyab / info->box_y + 0.5); |
461 |
> |
* (int)( fabs(pyab / info->box_y) + 0.5); |
462 |
|
pzab = pzab - info->box_z * copysign(1, pzab) |
463 |
< |
* int(pzab / info->box_z + 0.5); |
464 |
< |
|
465 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
466 |
< |
rabsq = constraintedDsqr[i]; |
467 |
< |
diffsq = pabsq - rabsq; |
463 |
> |
* (int)( fabs(pzab / info->box_z) + 0.5); |
464 |
> |
|
465 |
> |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
466 |
> |
|
467 |
> |
rabsq = constrainedDsqr[i]; |
468 |
> |
diffsq = rabsq - pabsq; |
469 |
|
|
470 |
|
// the original rattle code from alan tidesley |
471 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
472 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
473 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
474 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
475 |
< |
|
471 |
> |
if (fabs(diffsq) > (tol*rabsq*2)) { |
472 |
> |
rxab = oldPos[ax] - oldPos[bx]; |
473 |
> |
ryab = oldPos[ay] - oldPos[by]; |
474 |
> |
rzab = oldPos[az] - oldPos[bz]; |
475 |
> |
|
476 |
|
rxab = rxab - info->box_x * copysign(1, rxab) |
477 |
< |
* int(rxab / info->box_x + 0.5); |
477 |
> |
* (int)( fabs(rxab / info->box_x) + 0.5); |
478 |
|
ryab = ryab - info->box_y * copysign(1, ryab) |
479 |
< |
* int(ryab / info->box_y + 0.5); |
479 |
> |
* (int)( fabs(ryab / info->box_y) + 0.5); |
480 |
|
rzab = rzab - info->box_z * copysign(1, rzab) |
481 |
< |
* int(rzab / info->box_z + 0.5); |
481 |
> |
* (int)( fabs(rzab / info->box_z) + 0.5); |
482 |
|
|
483 |
|
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
484 |
+ |
|
485 |
|
rpabsq = rpab * rpab; |
486 |
|
|
487 |
|
|
488 |
|
if (rpabsq < (rabsq * -diffsq)){ |
489 |
+ |
|
490 |
|
#ifdef IS_MPI |
491 |
|
a = atoms[a]->getGlobalIndex(); |
492 |
|
b = atoms[b]->getGlobalIndex(); |
493 |
|
#endif //is_mpi |
494 |
|
sprintf( painCave.errMsg, |
495 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
495 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", |
496 |
|
a, b ); |
497 |
|
painCave.isFatal = 1; |
498 |
|
simError(); |
500 |
|
|
501 |
|
rma = 1.0 / atoms[a]->getMass(); |
502 |
|
rmb = 1.0 / atoms[b]->getMass(); |
503 |
< |
|
503 |
> |
|
504 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
505 |
+ |
|
506 |
|
dx = rxab * gab; |
507 |
|
dy = ryab * gab; |
508 |
|
dz = rzab * gab; |
509 |
|
|
510 |
< |
pos[3*a+0] += rma * dx; |
511 |
< |
pos[3*a+1] += rma * dy; |
512 |
< |
pos[3*a+2] += rma * dz; |
510 |
> |
pos[ax] += rma * dx; |
511 |
> |
pos[ay] += rma * dy; |
512 |
> |
pos[az] += rma * dz; |
513 |
|
|
514 |
< |
pos[3*b+0] -= rmb * dx; |
515 |
< |
pos[3*b+1] -= rmb * dy; |
516 |
< |
pos[3*b+2] -= rmb * dz; |
514 |
> |
pos[bx] -= rmb * dx; |
515 |
> |
pos[by] -= rmb * dy; |
516 |
> |
pos[bz] -= rmb * dz; |
517 |
|
|
518 |
|
dx = dx / dt; |
519 |
|
dy = dy / dt; |
520 |
|
dz = dz / dt; |
521 |
|
|
522 |
< |
vel[3*a+0] += rma * dx; |
523 |
< |
vel[3*a+1] += rma * dy; |
524 |
< |
vel[3*a+2] += rma * dz; |
522 |
> |
vel[ax] += rma * dx; |
523 |
> |
vel[ay] += rma * dy; |
524 |
> |
vel[az] += rma * dz; |
525 |
|
|
526 |
< |
vel[3*b+0] -= rmb * dx; |
527 |
< |
vel[3*b+1] -= rmb * dy; |
528 |
< |
vel[3*b+2] -= rmb * dz; |
526 |
> |
vel[bx] -= rmb * dx; |
527 |
> |
vel[by] -= rmb * dy; |
528 |
> |
vel[bz] -= rmb * dz; |
529 |
|
|
530 |
|
moving[a] = 1; |
531 |
|
moving[b] = 1; |
545 |
|
|
546 |
|
if( !done ){ |
547 |
|
|
548 |
< |
sprintf( painCae.errMsg, |
548 |
> |
sprintf( painCave.errMsg, |
549 |
|
"Constraint failure in constrainA, too many iterations: %d\n", |
550 |
< |
iterations ); |
550 |
> |
iteration ); |
551 |
|
painCave.isFatal = 1; |
552 |
|
simError(); |
553 |
|
} |
560 |
|
int done; |
561 |
|
double vxab, vyab, vzab; |
562 |
|
double rxab, ryab, rzab; |
563 |
< |
int a, b; |
563 |
> |
int a, b, ax, ay, az, bx, by, bz; |
564 |
|
double rma, rmb; |
565 |
|
double dx, dy, dz; |
566 |
|
double rabsq, pabsq, rvab; |
568 |
|
double gab; |
569 |
|
int iteration; |
570 |
|
|
571 |
< |
for(i=0; i<nAtom; i++){ |
571 |
> |
for(i=0; i<nAtoms; i++){ |
572 |
|
moving[i] = 0; |
573 |
|
moved[i] = 1; |
574 |
|
} |
575 |
|
|
576 |
|
done = 0; |
577 |
+ |
iteration = 0; |
578 |
|
while( !done && (iteration < maxIteration ) ){ |
579 |
|
|
580 |
+ |
done = 1; |
581 |
+ |
|
582 |
|
for(i=0; i<nConstrained; i++){ |
583 |
|
|
584 |
|
a = constrainedA[i]; |
585 |
|
b = constrainedB[i]; |
586 |
|
|
587 |
+ |
ax = (a*3) + 0; |
588 |
+ |
ay = (a*3) + 1; |
589 |
+ |
az = (a*3) + 2; |
590 |
+ |
|
591 |
+ |
bx = (b*3) + 0; |
592 |
+ |
by = (b*3) + 1; |
593 |
+ |
bz = (b*3) + 2; |
594 |
+ |
|
595 |
|
if( moved[a] || moved[b] ){ |
596 |
|
|
597 |
< |
vxab = vel[3*a+0] - vel[3*b+0]; |
598 |
< |
vyab = vel[3*a+1] - vel[3*b+1]; |
599 |
< |
vzab = vel[3*a+2] - vel[3*b+2]; |
597 |
> |
vxab = vel[ax] - vel[bx]; |
598 |
> |
vyab = vel[ay] - vel[by]; |
599 |
> |
vzab = vel[az] - vel[bz]; |
600 |
|
|
601 |
< |
rxab = pos[3*a+0] - pos[3*b+0];q |
602 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
603 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
601 |
> |
rxab = pos[ax] - pos[bx]; |
602 |
> |
ryab = pos[ay] - pos[by]; |
603 |
> |
rzab = pos[az] - pos[bz]; |
604 |
|
|
605 |
+ |
|
606 |
|
rxab = rxab - info->box_x * copysign(1, rxab) |
607 |
< |
* int(rxab / info->box_x + 0.5); |
607 |
> |
* (int)( fabs(rxab / info->box_x) + 0.5); |
608 |
|
ryab = ryab - info->box_y * copysign(1, ryab) |
609 |
< |
* int(ryab / info->box_y + 0.5); |
609 |
> |
* (int)( fabs(ryab / info->box_y) + 0.5); |
610 |
|
rzab = rzab - info->box_z * copysign(1, rzab) |
611 |
< |
* int(rzab / info->box_z + 0.5); |
612 |
< |
|
611 |
> |
* (int)( fabs(rzab / info->box_z) + 0.5); |
612 |
> |
|
613 |
|
rma = 1.0 / atoms[a]->getMass(); |
614 |
|
rmb = 1.0 / atoms[b]->getMass(); |
615 |
|
|
616 |
|
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
617 |
|
|
618 |
< |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
618 |
> |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
619 |
|
|
620 |
|
if (fabs(gab) > tol) { |
621 |
|
|
623 |
|
dy = ryab * gab; |
624 |
|
dz = rzab * gab; |
625 |
|
|
626 |
< |
vel[3*a+0] += rma * dx; |
627 |
< |
vel[3*a+1] += rma * dy; |
628 |
< |
vel[3*a+2] += rma * dz; |
626 |
> |
vel[ax] += rma * dx; |
627 |
> |
vel[ay] += rma * dy; |
628 |
> |
vel[az] += rma * dz; |
629 |
|
|
630 |
< |
vel[3*b+0] -= rmb * dx; |
631 |
< |
vel[3*b+1] -= rmb * dy; |
632 |
< |
vel[3*b+2] -= rmb * dz; |
630 |
> |
vel[bx] -= rmb * dx; |
631 |
> |
vel[by] -= rmb * dy; |
632 |
> |
vel[bz] -= rmb * dz; |
633 |
|
|
634 |
|
moving[a] = 1; |
635 |
|
moving[b] = 1; |
649 |
|
if( !done ){ |
650 |
|
|
651 |
|
|
652 |
< |
sprintf( painCae.errMsg, |
652 |
> |
sprintf( painCave.errMsg, |
653 |
|
"Constraint failure in constrainB, too many iterations: %d\n", |
654 |
< |
iterations ); |
654 |
> |
iteration ); |
655 |
|
painCave.isFatal = 1; |
656 |
|
simError(); |
657 |
|
} |
665 |
|
|
666 |
|
|
667 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
668 |
< |
double A[3][3] ){ |
668 |
> |
double A[9] ){ |
669 |
|
|
670 |
|
int i,j,k; |
671 |
|
double sinAngle; |
681 |
|
|
682 |
|
for(i=0; i<3; i++){ |
683 |
|
for(j=0; j<3; j++){ |
684 |
< |
tempA[j][i] = A[i][j]; |
684 |
> |
tempA[j][i] = A[3*i + j]; |
685 |
|
} |
686 |
|
} |
687 |
|
|
732 |
|
// A[][] = A[][] * transpose(rot[][]) |
733 |
|
|
734 |
|
|
735 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
735 |
> |
// NOte for as yet unknown reason, we are performing the |
736 |
|
// calculation as: |
737 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
738 |
|
|
739 |
|
for(i=0; i<3; i++){ |
740 |
|
for(j=0; j<3; j++){ |
741 |
< |
A[j][i] = 0.0; |
741 |
> |
A[3*j + i] = 0.0; |
742 |
|
for(k=0; k<3; k++){ |
743 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
743 |
> |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
744 |
|
} |
745 |
|
} |
746 |
|
} |