--- trunk/OOPSE/libmdtools/Integrator.cpp 2003/06/19 22:02:44 559 +++ trunk/OOPSE/libmdtools/Integrator.cpp 2003/07/15 17:57:04 614 @@ -1,5 +1,6 @@ #include #include +#include #ifdef IS_MPI #include "mpiSimulation.hpp" @@ -10,7 +11,7 @@ Integrator::Integrator( SimInfo* theInfo, ForceFields* #include "simError.h" -Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ +Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ info = theInfo; myFF = the_ff; @@ -33,7 +34,7 @@ Integrator::Integrator( SimInfo* theInfo, ForceFields* constrainedDsqr = NULL; moving = NULL; moved = NULL; - prePos = NULL; + oldPos = NULL; nConstrained = 0; @@ -48,7 +49,7 @@ Integrator::~Integrator() { delete[] constrainedDsqr; delete[] moving; delete[] moved; - delete[] prePos; + delete[] oldPos; } } @@ -71,9 +72,9 @@ void Integrator::checkConstraints( void ){ for(int j=0; jis_constrained(); - + if(constrained){ - + dummy_plug = theArray[j]->get_constraint(); temp_con[nConstrained].set_a( dummy_plug->get_a() ); temp_con[nConstrained].set_b( dummy_plug->get_b() ); @@ -81,7 +82,7 @@ void Integrator::checkConstraints( void ){ nConstrained++; constrained = 0; - } + } } theArray = (SRI**) molecules[i].getMyBends(); @@ -136,6 +137,7 @@ void Integrator::checkConstraints( void ){ constrainedA[i] = temp_con[i].get_a(); constrainedB[i] = temp_con[i].get_b(); constrainedDsqr[i] = temp_con[i].get_dsqr(); + } @@ -146,7 +148,7 @@ void Integrator::checkConstraints( void ){ moving = new int[nAtoms]; moved = new int[nAtoms]; - prePos = new double[nAtoms*3]; + oldPos = new double[nAtoms*3]; } delete[] temp_con; @@ -156,24 +158,7 @@ void Integrator::integrate( void ){ void Integrator::integrate( void ){ int i, j; // loop counters - double kE = 0.0; // the kinetic energy - double rot_kE; - double trans_kE; - int tl; // the time loop conter - double dt2; // half the dt - double vx, vy, vz; // the velocities - double vx2, vy2, vz2; // the square of the velocities - double rx, ry, rz; // the postitions - - double ji[3]; // the body frame angular momentum - double jx2, jy2, jz2; // the square of the angular momentums - double Tb[3]; // torque in the body frame - double angle; // the angle through which to rotate the rotation matrix - double A[3][3]; // the rotation matrix - double press[9]; - - double dt = info->dt; double runTime = info->run_time; double sampleTime = info->sampleTime; double statusTime = info->statusTime; @@ -188,11 +173,13 @@ void Integrator::integrate( void ){ int isError; tStats = new Thermo( info ); - e_out = new StatWriter( info ); - dump_out = new DumpWriter( info ); + statOut = new StatWriter( info ); + dumpOut = new DumpWriter( info ); - Atom** atoms = info->atoms; + atoms = info->atoms; DirectionalAtom* dAtom; + + dt = info->dt; dt2 = 0.5 * dt; // initialize the forces before the first step @@ -204,8 +191,8 @@ void Integrator::integrate( void ){ tStats->velocitize(); } - dump_out->writeDump( 0.0 ); - e_out->writeStat( 0.0 ); + dumpOut->writeDump( 0.0 ); + statOut->writeStat( 0.0 ); calcPot = 0; calcStress = 0; @@ -229,7 +216,7 @@ void Integrator::integrate( void ){ calcPot = 1; calcStress = 1; } - + integrateStep( calcPot, calcStress ); currTime += dt; @@ -242,12 +229,12 @@ void Integrator::integrate( void ){ } if( currTime >= currSample ){ - dump_out->writeDump( currTime ); + dumpOut->writeDump( currTime ); currSample += sampleTime; } if( currTime >= currStatus ){ - e_out->writeStat( time * dt ); + statOut->writeStat( currTime ); calcPot = 0; calcStress = 0; currStatus += statusTime; @@ -261,195 +248,214 @@ void Integrator::integrate( void ){ } - dump_out->writeFinal(); + dumpOut->writeFinal(currTime); - delete dump_out; - delete e_out; + delete dumpOut; + delete statOut; } void Integrator::integrateStep( int calcPot, int calcStress ){ + + // Position full step, and velocity half step - //preMove(); + preMove(); moveA(); if( nConstrained ) constrainA(); + +#ifdef IS_MPI + strcpy( checkPointMsg, "Succesful moveA\n" ); + MPIcheckPoint(); +#endif // is_mpi + + // calc forces myFF->doForces(calcPot,calcStress); +#ifdef IS_MPI + strcpy( checkPointMsg, "Succesful doForces\n" ); + MPIcheckPoint(); +#endif // is_mpi + + // finish the velocity half step moveB(); if( nConstrained ) constrainB(); - + +#ifdef IS_MPI + strcpy( checkPointMsg, "Succesful moveB\n" ); + MPIcheckPoint(); +#endif // is_mpi + + } void Integrator::moveA( void ){ - int i,j,k; - int atomIndex, aMatIndex; + int i, j; DirectionalAtom* dAtom; - double Tb[3]; - double ji[3]; + double Tb[3], ji[3]; + double A[3][3], I[3][3]; + double angle; + double vel[3], pos[3], frc[3]; + double mass; for( i=0; igetMass() ) * eConvert; - // position whole step - for( j=atomIndex; j<(atomIndex+3); j++ ) + atoms[i]->getVel( vel ); + atoms[i]->getPos( pos ); + atoms[i]->getFrc( frc ); + + mass = atoms[i]->getMass(); + + for (j=0; j < 3; j++) { + // velocity half step + vel[j] += ( dt2 * frc[j] / mass ) * eConvert; + // position whole step pos[j] += dt * vel[j]; + } - + atoms[i]->setVel( vel ); + atoms[i]->setPos( pos ); + if( atoms[i]->isDirectional() ){ dAtom = (DirectionalAtom *)atoms[i]; // get and convert the torque to body frame - Tb[0] = dAtom->getTx(); - Tb[1] = dAtom->getTy(); - Tb[2] = dAtom->getTz(); - + dAtom->getTrq( Tb ); dAtom->lab2Body( Tb ); - + // get the angular momentum, and propagate a half step + + dAtom->getJ( ji ); + + for (j=0; j < 3; j++) + ji[j] += (dt2 * Tb[j]) * eConvert; - ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; - ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; - ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; - // use the angular velocities to propagate the rotation matrix a // full time step - + + dAtom->getA(A); + dAtom->getI(I); + // rotate about the x-axis - angle = dt2 * ji[0] / dAtom->getIxx(); - this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); - + angle = dt2 * ji[0] / I[0][0]; + this->rotate( 1, 2, angle, ji, A ); + // rotate about the y-axis - angle = dt2 * ji[1] / dAtom->getIyy(); - this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); + angle = dt2 * ji[1] / I[1][1]; + this->rotate( 2, 0, angle, ji, A ); // rotate about the z-axis - angle = dt * ji[2] / dAtom->getIzz(); - this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); + angle = dt * ji[2] / I[2][2]; + this->rotate( 0, 1, angle, ji, A); // rotate about the y-axis - angle = dt2 * ji[1] / dAtom->getIyy(); - this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); + angle = dt2 * ji[1] / I[1][1]; + this->rotate( 2, 0, angle, ji, A ); // rotate about the x-axis - angle = dt2 * ji[0] / dAtom->getIxx(); - this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); + angle = dt2 * ji[0] / I[0][0]; + this->rotate( 1, 2, angle, ji, A ); - dAtom->setJx( ji[0] ); - dAtom->setJy( ji[1] ); - dAtom->setJz( ji[2] ); - } - + + dAtom->setJ( ji ); + dAtom->setA( A ); + + } } } void Integrator::moveB( void ){ - int i,j,k; - int atomIndex; + int i, j; DirectionalAtom* dAtom; - double Tb[3]; - double ji[3]; + double Tb[3], ji[3]; + double vel[3], frc[3]; + double mass; for( i=0; igetVel( vel ); + atoms[i]->getFrc( frc ); - // velocity half step - for( j=atomIndex; j<(atomIndex+3); j++ ) - vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; + mass = atoms[i]->getMass(); + // velocity half step + for (j=0; j < 3; j++) + vel[j] += ( dt2 * frc[j] / mass ) * eConvert; + + atoms[i]->setVel( vel ); + if( atoms[i]->isDirectional() ){ - + dAtom = (DirectionalAtom *)atoms[i]; - - // get and convert the torque to body frame - - Tb[0] = dAtom->getTx(); - Tb[1] = dAtom->getTy(); - Tb[2] = dAtom->getTz(); - + + // get and convert the torque to body frame + + dAtom->getTrq( Tb ); dAtom->lab2Body( Tb ); + + // get the angular momentum, and propagate a half step + + dAtom->getJ( ji ); + + for (j=0; j < 3; j++) + ji[j] += (dt2 * Tb[j]) * eConvert; - // get the angular momentum, and complete the angular momentum - // half step - - ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; - ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; - ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; - - jx2 = ji[0] * ji[0]; - jy2 = ji[1] * ji[1]; - jz2 = ji[2] * ji[2]; - - dAtom->setJx( ji[0] ); - dAtom->setJy( ji[1] ); - dAtom->setJz( ji[2] ); + + dAtom->setJ( ji ); } } - } void Integrator::preMove( void ){ - int i; + int i, j; + double pos[3]; if( nConstrained ){ - if( oldAtoms != nAtoms ){ - - // save oldAtoms to check for lode balanceing later on. - - oldAtoms = nAtoms; - - delete[] moving; - delete[] moved; - delete[] oldPos; - - moving = new int[nAtoms]; - moved = new int[nAtoms]; - - oldPos = new double[nAtoms*3]; + + for(i=0; i < nAtoms; i++) { + + atoms[i]->getPos( pos ); + + for (j = 0; j < 3; j++) { + oldPos[3*i + j] = pos[j]; + } + } - - for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; - } -} + } +} void Integrator::constrainA(){ int i,j,k; int done; - double pxab, pyab, pzab; - double rxab, ryab, rzab; - int a, b; + double posA[3], posB[3]; + double velA[3], velB[3]; + double pab[3]; + double rab[3]; + int a, b, ax, ay, az, bx, by, bz; double rma, rmb; double dx, dy, dz; + double rpab; double rabsq, pabsq, rpabsq; double diffsq; double gab; int iteration; - - - for( i=0; igetPos( posA ); + atoms[b]->getPos( posB ); + + for (j = 0; j < 3; j++ ) + pab[j] = posA[j] - posB[j]; + + //periodic boundary condition - //periodic boundary condition - pxab = pxab - info->box_x * copysign(1, pxab) - * int(pxab / info->box_x + 0.5); - pyab = pyab - info->box_y * copysign(1, pyab) - * int(pyab / info->box_y + 0.5); - pzab = pzab - info->box_z * copysign(1, pzab) - * int(pzab / info->box_z + 0.5); - - pabsq = pxab * pxab + pyab * pyab + pzab * pzab; - rabsq = constraintedDsqr[i]; - diffsq = pabsq - rabsq; + info->wrapVector( pab ); + pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; + + rabsq = constrainedDsqr[i]; + diffsq = rabsq - pabsq; + // the original rattle code from alan tidesley - if (fabs(diffsq) > tol*rabsq*2) { - rxab = oldPos[3*a+0] - oldPos[3*b+0]; - ryab = oldPos[3*a+1] - oldPos[3*b+1]; - rzab = oldPos[3*a+2] - oldPos[3*b+2]; - - rxab = rxab - info->box_x * copysign(1, rxab) - * int(rxab / info->box_x + 0.5); - ryab = ryab - info->box_y * copysign(1, ryab) - * int(ryab / info->box_y + 0.5); - rzab = rzab - info->box_z * copysign(1, rzab) - * int(rzab / info->box_z + 0.5); + if (fabs(diffsq) > (tol*rabsq*2)) { + rab[0] = oldPos[ax] - oldPos[bx]; + rab[1] = oldPos[ay] - oldPos[by]; + rab[2] = oldPos[az] - oldPos[bz]; - rpab = rxab * pxab + ryab * pyab + rzab * pzab; + info->wrapVector( rab ); + + rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; + rpabsq = rpab * rpab; if (rpabsq < (rabsq * -diffsq)){ + #ifdef IS_MPI a = atoms[a]->getGlobalIndex(); b = atoms[b]->getGlobalIndex(); #endif //is_mpi sprintf( painCave.errMsg, - "Constraint failure in constrainA at atom %d and %d\n.", + "Constraint failure in constrainA at atom %d and %d.\n", a, b ); painCave.isFatal = 1; simError(); @@ -509,32 +519,45 @@ void Integrator::constrainA(){ rma = 1.0 / atoms[a]->getMass(); rmb = 1.0 / atoms[b]->getMass(); - + gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); - dx = rxab * gab; - dy = ryab * gab; - dz = rzab * gab; - pos[3*a+0] += rma * dx; - pos[3*a+1] += rma * dy; - pos[3*a+2] += rma * dz; + dx = rab[0] * gab; + dy = rab[1] * gab; + dz = rab[2] * gab; - pos[3*b+0] -= rmb * dx; - pos[3*b+1] -= rmb * dy; - pos[3*b+2] -= rmb * dz; + posA[0] += rma * dx; + posA[1] += rma * dy; + posA[2] += rma * dz; + atoms[a]->setPos( posA ); + + posB[0] -= rmb * dx; + posB[1] -= rmb * dy; + posB[2] -= rmb * dz; + + atoms[b]->setPos( posB ); + dx = dx / dt; dy = dy / dt; dz = dz / dt; - vel[3*a+0] += rma * dx; - vel[3*a+1] += rma * dy; - vel[3*a+2] += rma * dz; + atoms[a]->getVel( velA ); - vel[3*b+0] -= rmb * dx; - vel[3*b+1] -= rmb * dy; - vel[3*b+2] -= rmb * dz; + velA[0] += rma * dx; + velA[1] += rma * dy; + velA[2] += rma * dz; + atoms[a]->setVel( velA ); + + atoms[b]->getVel( velB ); + + velB[0] -= rmb * dx; + velB[1] -= rmb * dy; + velB[2] -= rmb * dz; + + atoms[b]->setVel( velB ); + moving[a] = 1; moving[b] = 1; done = 0; @@ -553,9 +576,9 @@ void Integrator::constrainA(){ if( !done ){ - sprintf( painCae.errMsg, + sprintf( painCave.errMsg, "Constraint failure in constrainA, too many iterations: %d\n", - iterations ); + iteration ); painCave.isFatal = 1; simError(); } @@ -566,9 +589,11 @@ void Integrator::constrainB( void ){ int i,j,k; int done; + double posA[3], posB[3]; + double velA[3], velB[3]; double vxab, vyab, vzab; - double rxab, ryab, rzab; - int a, b; + double rab[3]; + int a, b, ax, ay, az, bx, by, bz; double rma, rmb; double dx, dy, dz; double rabsq, pabsq, rvab; @@ -576,56 +601,71 @@ void Integrator::constrainB( void ){ double gab; int iteration; - for(i=0; ibox_x * copysign(1, rxab) - * int(rxab / info->box_x + 0.5); - ryab = ryab - info->box_y * copysign(1, ryab) - * int(ryab / info->box_y + 0.5); - rzab = rzab - info->box_z * copysign(1, rzab) - * int(rzab / info->box_z + 0.5); + atoms[a]->getVel( velA ); + atoms[b]->getVel( velB ); + + vxab = velA[0] - velB[0]; + vyab = velA[1] - velB[1]; + vzab = velA[2] - velB[2]; + atoms[a]->getPos( posA ); + atoms[b]->getPos( posB ); + + for (j = 0; j < 3; j++) + rab[j] = posA[j] - posB[j]; + + info->wrapVector( rab ); + rma = 1.0 / atoms[a]->getMass(); rmb = 1.0 / atoms[b]->getMass(); - rvab = rxab * vxab + ryab * vyab + rzab * vzab; + rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; - gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); + gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); if (fabs(gab) > tol) { - dx = rxab * gab; - dy = ryab * gab; - dz = rzab * gab; - - vel[3*a+0] += rma * dx; - vel[3*a+1] += rma * dy; - vel[3*a+2] += rma * dz; + dx = rab[0] * gab; + dy = rab[1] * gab; + dz = rab[2] * gab; + + velA[0] += rma * dx; + velA[1] += rma * dy; + velA[2] += rma * dz; - vel[3*b+0] -= rmb * dx; - vel[3*b+1] -= rmb * dy; - vel[3*b+2] -= rmb * dz; + atoms[a]->setVel( velA ); + + velB[0] -= rmb * dx; + velB[1] -= rmb * dy; + velB[2] -= rmb * dz; + + atoms[b]->setVel( velB ); moving[a] = 1; moving[b] = 1; @@ -641,25 +681,19 @@ void Integrator::constrainB( void ){ iteration++; } - + if( !done ){ - sprintf( painCae.errMsg, + sprintf( painCave.errMsg, "Constraint failure in constrainB, too many iterations: %d\n", - iterations ); + iteration ); painCave.isFatal = 1; simError(); } } - - - - - - void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], double A[3][3] ){ @@ -728,7 +762,7 @@ void Integrator::rotate( int axes1, int axes2, double // A[][] = A[][] * transpose(rot[][]) - // NOte for as yet unknown reason, we are setting the performing the + // NOte for as yet unknown reason, we are performing the // calculation as: // transpose(A[][]) = transpose(A[][]) * transpose(rot[][])