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#include <cmath> |
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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void NPTi::moveA() { |
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int i,j,k; |
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int atomIndex, aMatIndex; |
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int i, j; |
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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 Tb[3], ji[3]; |
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double A[3][3], I[3][3]; |
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double angle, mass; |
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double vel[3], pos[3], frc[3]; |
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double rj[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double angle; |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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// first evolve chi a half step |
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// first evolve chi a half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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atoms[i]->getVel( vel ); |
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atoms[i]->getPos( pos ); |
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atoms[i]->getFrc( frc ); |
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// position whole step |
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mass = atoms[i]->getMass(); |
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rj[0] = pos[atomIndex]; |
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rj[1] = pos[atomIndex+1]; |
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rj[2] = pos[atomIndex+2]; |
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for (j=0; j < 3; j++) { |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
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rj[j] = pos[j]; |
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} |
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atoms[i]->setVel( vel ); |
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info->wrapVector(rj); |
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pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]); |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]); |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]); |
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for (j = 0; j < 3; j++) |
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pos[j] += dt * (vel[j] + eta*rj[j]); |
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atoms[i]->setPos( pos ); |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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// get and convert the torque to body frame |
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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dAtom->getJ( ji ); |
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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dAtom->getA(A); |
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dAtom->getI(I); |
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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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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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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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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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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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angle = dt * ji[2] / I[2][2]; |
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this->rotate( 0, 1, angle, ji, A); |
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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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angle = dt2 * ji[1] / I[1][1]; |
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this->rotate( 2, 0, angle, ji, A ); |
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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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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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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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} |
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dAtom->setJ( ji ); |
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dAtom->setA( A ); |
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} |
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} |
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// Scale the box after all the positions have been moved: |
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info->scaleBox(exp(dt*eta)); |
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cerr << "eta = " << eta |
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<< "; exp(dt*eta) = " << exp(eta*dt) << "\n"; |
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info->scaleBox(exp(dt*eta)); |
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} |
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void NPTi::moveB( void ){ |
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int i,j,k; |
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int atomIndex; |
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int i, j; |
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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 Tb[3], ji[3]; |
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double vel[3], frc[3]; |
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double mass; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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instaVol = tStats->getVolume(); |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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mass = atoms[i]->getMass(); |
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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for (j=0; j < 3; j++) |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
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atoms[i]->setVel( vel ); |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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// get and convert the torque to body frame |
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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// get and convert the torque to body frame |
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and complete the angular momentum |
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// half step |
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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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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// get the angular momentum, and propagate a half step |
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dAtom->getJ( ji ); |
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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dAtom->setJ( ji ); |
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} |
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} |
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} |
