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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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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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nConstrained = 0; |
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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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} |
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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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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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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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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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MPIcheckPoint(); |
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#endif // is_mpi |
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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 ); |
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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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dump_out->writeFinal(); |
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dumpOut->writeFinal(); |
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delete dump_out; |
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delete e_out; |
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delete dumpOut; |
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delete statOut; |
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} |
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void Integrator::integrateStep( int calcPot, int calcStress ){ |
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// Position full step, and velocity half step |
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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; |
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double Tb[3]; |
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double ji[3]; |
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double angle; |
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
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ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
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jx2 = ji[0] * ji[0]; |
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jy2 = ji[1] * ji[1]; |
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jz2 = ji[2] * ji[2]; |
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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int i; |
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if( nConstrained ){ |
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if( oldAtoms != nAtoms ){ |
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// if( oldAtoms != nAtoms ){ |
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// save oldAtoms to check for lode balanceing later on. |
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// // save oldAtoms to check for lode balanceing later on. |
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oldAtoms = nAtoms; |
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// oldAtoms = nAtoms; |
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delete[] moving; |
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delete[] moved; |
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delete[] oldPos; |
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// delete[] moving; |
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// delete[] moved; |
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// delete[] oldPos; |
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moving = new int[nAtoms]; |
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moved = new int[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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// oldPos = new double[nAtoms*3]; |
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// } |
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for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
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} |
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int a, b; |
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double rma, rmb; |
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double dx, dy, dz; |
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double rpab; |
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double rabsq, pabsq, rpabsq; |
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double diffsq; |
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double gab; |
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//periodic boundary condition |
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pxab = pxab - info->box_x * copysign(1, pxab) |
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* int(pxab / info->box_x + 0.5); |
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* int( fabs(pxab) / info->box_x + 0.5); |
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pyab = pyab - info->box_y * copysign(1, pyab) |
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* int(pyab / info->box_y + 0.5); |
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* int( fabs(pyab) / info->box_y + 0.5); |
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pzab = pzab - info->box_z * copysign(1, pzab) |
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* int(pzab / info->box_z + 0.5); |
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* int( fabs(pzab) / info->box_z + 0.5); |
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pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
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rabsq = constraintedDsqr[i]; |
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rabsq = constrainedDsqr[i]; |
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diffsq = pabsq - rabsq; |
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// the original rattle code from alan tidesley |
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rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
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rxab = rxab - info->box_x * copysign(1, rxab) |
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* int(rxab / info->box_x + 0.5); |
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* int( fabs(rxab) / info->box_x + 0.5); |
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ryab = ryab - info->box_y * copysign(1, ryab) |
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* int(ryab / info->box_y + 0.5); |
486 |
> |
* int( fabs(ryab) / info->box_y + 0.5); |
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rzab = rzab - info->box_z * copysign(1, rzab) |
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* int(rzab / info->box_z + 0.5); |
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> |
* int( fabs(rzab) / info->box_z + 0.5); |
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rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
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rpabsq = rpab * rpab; |
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if( !done ){ |
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sprintf( painCae.errMsg, |
552 |
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sprintf( painCave.errMsg, |
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"Constraint failure in constrainA, too many iterations: %d\n", |
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iterations ); |
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iteration ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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double gab; |
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int iteration; |
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for(i=0; i<nAtom; i++){ |
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> |
for(i=0; i<nAtoms; i++){ |
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moving[i] = 0; |
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moved[i] = 1; |
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} |
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done = 0; |
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iteration = 0; |
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while( !done && (iteration < maxIteration ) ){ |
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for(i=0; i<nConstrained; i++){ |
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vyab = vel[3*a+1] - vel[3*b+1]; |
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vzab = vel[3*a+2] - vel[3*b+2]; |
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rxab = pos[3*a+0] - pos[3*b+0];q |
595 |
> |
rxab = pos[3*a+0] - pos[3*b+0]; |
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ryab = pos[3*a+1] - pos[3*b+1]; |
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rzab = pos[3*a+2] - pos[3*b+2]; |
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rxab = rxab - info->box_x * copysign(1, rxab) |
600 |
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* int(rxab / info->box_x + 0.5); |
600 |
> |
* int( fabs(rxab) / info->box_x + 0.5); |
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ryab = ryab - info->box_y * copysign(1, ryab) |
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* int(ryab / info->box_y + 0.5); |
602 |
> |
* int( fabs(ryab) / info->box_y + 0.5); |
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rzab = rzab - info->box_z * copysign(1, rzab) |
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* int(rzab / info->box_z + 0.5); |
604 |
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* int( fabs(rzab) / info->box_z + 0.5); |
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rma = 1.0 / atoms[a]->getMass(); |
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rmb = 1.0 / atoms[b]->getMass(); |
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rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
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gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
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> |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
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if (fabs(gab) > tol) { |
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if( !done ){ |
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sprintf( painCae.errMsg, |
645 |
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sprintf( painCave.errMsg, |
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"Constraint failure in constrainB, too many iterations: %d\n", |
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iterations ); |
647 |
> |
iteration ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
661 |
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double A[3][3] ){ |
661 |
> |
double A[9] ){ |
662 |
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int i,j,k; |
664 |
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double sinAngle; |
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675 |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
677 |
< |
tempA[j][i] = A[i][j]; |
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> |
tempA[j][i] = A[3*i + j]; |
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} |
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} |
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// A[][] = A[][] * transpose(rot[][]) |
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727 |
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728 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
728 |
> |
// NOte for as yet unknown reason, we are performing the |
729 |
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// calculation as: |
730 |
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// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
731 |
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732 |
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for(i=0; i<3; i++){ |
733 |
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for(j=0; j<3; j++){ |
734 |
< |
A[j][i] = 0.0; |
734 |
> |
A[3*j + i] = 0.0; |
735 |
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for(k=0; k<3; k++){ |
736 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
736 |
> |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
737 |
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} |
738 |
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} |
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} |