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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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#include "SimInfo.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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|
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// Basic isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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// The NPTim variant scales the molecular center-of-mass coordinates |
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// instead of the atomic coordinates |
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|
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NPTim::NPTim ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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{ |
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chi = 0.0; |
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eta = 0.0; |
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have_tau_thermostat = 0; |
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have_tau_barostat = 0; |
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have_target_temp = 0; |
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have_target_pressure = 0; |
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} |
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|
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void NPTim::moveA() { |
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|
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int i,j,k; |
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int nInMol, aMatIndex; |
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DirectionalAtom* dAtom; |
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Atom** theAtoms; |
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Molecule** myMols; |
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double Tb[3]; |
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double ji[3]; |
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double rc[3]; |
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double mass; |
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double rx, ry, rz, vx, vy, vz, fx, fy, fz; |
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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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|
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nMols = info->n_mol; |
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myMols = info->molecules; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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|
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// first evolve chi a half step |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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|
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for( i = 0; i < nMols; i++) { |
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|
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myMols[i].getCOM(rc); |
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|
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nInMol = myMols[i]->getNAtoms(); |
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theAtoms = myMols[i]->getMyAtoms(); |
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|
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// find the minimum image coordinates of the molecular centers of mass: |
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|
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info->wrapVector(rc); |
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|
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for (j = 0; j < nInMol; j++) { |
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|
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if(theAtoms[j] != NULL) { |
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|
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aMatIndex = 9 * theAtoms[j]->getIndex(); |
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|
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mass = theAtoms[j]->getMass(); |
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|
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vx = theAtoms[j]->get_vx(); |
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vy = theAtoms[j]->get_vy(); |
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vz = theAtoms[j]->get_vz(); |
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|
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fx = theAtoms[j]->getFx(); |
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fy = theAtoms[j]->getFy(); |
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fz = theAtoms[j]->getFz(); |
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|
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rx = theAtoms[j]->getX(); |
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ry = theAtoms[j]->getY(); |
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rz = theAtoms[j]->getZ(); |
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|
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// velocity half step |
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|
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vx += dt2 * ((fx / mass)*eConvert - vx*(chi+eta)); |
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vy += dt2 * ((fy / mass)*eConvert - vy*(chi+eta)); |
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vz += dt2 * ((fz / mass)*eConvert - vz*(chi+eta)); |
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|
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// position whole step |
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|
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rx += dt*(vx + eta*rc[0]); |
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ry += dt*(vy + eta*rc[1]); |
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rz += dt*(vz + eta*rc[2]); |
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|
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theAtoms[j]->set_vx(vx); |
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theAtoms[j]->set_vy(vy); |
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theAtoms[j]->set_vz(vz); |
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|
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theAtoms[j]->setX(rx); |
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theAtoms[j]->setY(ry); |
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theAtoms[j]->setZ(rz); |
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|
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if( theAtoms[j]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)theAtoms[j]; |
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|
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// get and convert the torque to body frame |
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|
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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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|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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} |
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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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|
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cerr << "eta = " << eta |
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<< "; exp(dt*eta) = " << exp(eta*dt) << "\n"; |
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|
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info->scaleBox(exp(dt*eta)); |
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} |
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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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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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|
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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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|
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if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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|
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// get and convert the torque to body frame |
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|
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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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|
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and complete the angular momentum |
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// half step |
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|
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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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|
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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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|
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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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} |
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} |
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|
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int NPTi::readyCheck() { |
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|
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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|
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if (!have_target_temp) { |
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sprintf( painCave.errMsg, |
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"NPTi error: You can't use the NPTi integrator\n" |
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" without a targetTemp!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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if (!have_target_pressure) { |
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sprintf( painCave.errMsg, |
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"NPTi error: You can't use the NPTi integrator\n" |
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" without a targetPressure!\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauThermostat. |
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|
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if (!have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NPTi error: If you use the NPTi\n" |
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" integrator, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We must set tauBarostat. |
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|
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if (!have_tau_barostat) { |
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sprintf( painCave.errMsg, |
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"NPTi error: If you use the NPTi\n" |
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" integrator, you must set tauBarostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We need NkBT a lot, so just set it here: |
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|
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NkBT = (double)info->ndf * kB * targetTemp; |
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|
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return 1; |
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} |
