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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 "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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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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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
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Integrator( theInfo, the_ff ) |
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> |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
> |
T( theInfo, the_ff ) |
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{ |
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chi = 0.0; |
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eta = 0.0; |
32 |
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integralOfChidt = 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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have_chi_tolerance = 0; |
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have_eta_tolerance = 0; |
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have_pos_iter_tolerance = 0; |
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|
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oldPos = new double[3*nAtoms]; |
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oldVel = new double[3*nAtoms]; |
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oldJi = new double[3*nAtoms]; |
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#ifdef IS_MPI |
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Nparticles = mpiSim->getTotAtoms(); |
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#else |
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Nparticles = theInfo->n_atoms; |
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#endif |
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|
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} |
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|
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< |
void NPTi::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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template<typename T> NPTi<T>::~NPTi() { |
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delete[] oldPos; |
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delete[] oldVel; |
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delete[] oldJi; |
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} |
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|
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template<typename T> void NPTi<T>::moveA() { |
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|
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//new version of NPTi |
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int i, j, k; |
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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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|
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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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double tt2, tb2, scaleFactor; |
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double COM[3]; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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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) / (NkBT*tb2)); |
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|
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tStats->getCOM(COM); |
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|
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//evolve velocity half step |
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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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|
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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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|
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// position whole step |
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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|
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for( j=atomIndex; j<(atomIndex+3); j=j+3 ) { |
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rj[0] = pos[j]; |
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rj[1] = pos[j+1]; |
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rj[2] = pos[j+2]; |
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mass = atoms[i]->getMass(); |
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|
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info->wrapVector(rj); |
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|
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pos[j] += dt * (vel[j] + eta*rj[0]); |
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pos[j+1] += dt * (vel[j+1] + eta*rj[1]); |
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pos[j+2] += dt * (vel[j+2] + eta*rj[2]); |
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for (j=0; j < 3; j++) { |
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// velocity half step (use chi from previous step here): |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
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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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info->scaleBox(exp(dt*eta)); |
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atoms[i]->setVel( vel ); |
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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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|
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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->getTrq( Tb ); |
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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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dAtom->getJ( ji ); |
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|
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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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|
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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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|
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dAtom->getA(A); |
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dAtom->getI(I); |
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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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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
123 |
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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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angle = dt2 * ji[1] / I[1][1]; |
126 |
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this->rotate( 2, 0, angle, ji, A ); |
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|
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// rotate about the z-axis |
129 |
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angle = dt * ji[2] / dAtom->getIzz(); |
130 |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
129 |
> |
angle = dt * ji[2] / I[2][2]; |
130 |
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this->rotate( 0, 1, angle, ji, A); |
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|
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// rotate about the y-axis |
133 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
134 |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
133 |
> |
angle = dt2 * ji[1] / I[1][1]; |
134 |
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this->rotate( 2, 0, angle, ji, A ); |
135 |
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|
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// rotate about the x-axis |
137 |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
138 |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
137 |
> |
angle = dt2 * ji[0] / I[0][0]; |
138 |
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this->rotate( 1, 2, angle, ji, A ); |
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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] ); |
140 |
> |
dAtom->setJ( ji ); |
141 |
> |
dAtom->setA( A ); |
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> |
} |
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> |
} |
144 |
> |
|
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> |
// evolve chi and eta half step |
146 |
> |
|
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> |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
148 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
149 |
> |
|
150 |
> |
//calculate the integral of chidt |
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integralOfChidt += dt2*chi; |
152 |
> |
|
153 |
> |
//save the old positions |
154 |
> |
for(i = 0; i < nAtoms; i++){ |
155 |
> |
atoms[i]->getPos(pos); |
156 |
> |
for(j = 0; j < 3; j++) |
157 |
> |
oldPos[i*3 + j] = pos[j]; |
158 |
> |
} |
159 |
> |
|
160 |
> |
//the first estimation of r(t+dt) is equal to r(t) |
161 |
> |
|
162 |
> |
for(k = 0; k < 4; k ++){ |
163 |
> |
|
164 |
> |
for(i =0 ; i < nAtoms; i++){ |
165 |
> |
|
166 |
> |
atoms[i]->getVel(vel); |
167 |
> |
atoms[i]->getPos(pos); |
168 |
> |
|
169 |
> |
for(j = 0; j < 3; j++) |
170 |
> |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
171 |
> |
|
172 |
> |
for(j = 0; j < 3; j++) |
173 |
> |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
174 |
> |
|
175 |
> |
atoms[i]->setPos( pos ); |
176 |
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} |
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|
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if (nConstrained){ |
179 |
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constrainA(); |
180 |
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} |
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} |
182 |
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|
183 |
+ |
|
184 |
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// Scale the box after all the positions have been moved: |
185 |
+ |
|
186 |
+ |
scaleFactor = exp(dt*eta); |
187 |
+ |
|
188 |
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
189 |
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sprintf( painCave.errMsg, |
190 |
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"NPTi error: Attempting a Box scaling of more than 10 percent" |
191 |
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" check your tauBarostat, as it is probably too small!\n" |
192 |
+ |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
193 |
+ |
); |
194 |
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painCave.isFatal = 1; |
195 |
+ |
simError(); |
196 |
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} else { |
197 |
+ |
info->scaleBox(scaleFactor); |
198 |
+ |
} |
199 |
+ |
|
200 |
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} |
201 |
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|
202 |
< |
void NPTi::moveB( void ){ |
203 |
< |
int i,j,k; |
204 |
< |
int atomIndex; |
202 |
> |
template<typename T> void NPTi<T>::moveB( void ){ |
203 |
> |
|
204 |
> |
//new version of NPTi |
205 |
> |
int i, j, k; |
206 |
|
DirectionalAtom* dAtom; |
207 |
< |
double Tb[3]; |
208 |
< |
double ji[3]; |
209 |
< |
double instaTemp, instaPress, instaVol; |
207 |
> |
double Tb[3], ji[3]; |
208 |
> |
double vel[3], frc[3]; |
209 |
> |
double mass; |
210 |
> |
|
211 |
> |
double instTemp, instPress, instVol; |
212 |
|
double tt2, tb2; |
213 |
+ |
double oldChi, prevChi; |
214 |
+ |
double oldEta, preEta; |
215 |
|
|
216 |
|
tt2 = tauThermostat * tauThermostat; |
217 |
|
tb2 = tauBarostat * tauBarostat; |
218 |
|
|
149 |
– |
instaTemp = tStats->getTemperature(); |
150 |
– |
instaPress = tStats->getPressure(); |
151 |
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instaVol = tStats->getVolume(); |
219 |
|
|
220 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
221 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
222 |
< |
|
220 |
> |
// Set things up for the iteration: |
221 |
> |
|
222 |
> |
oldChi = chi; |
223 |
> |
oldEta = eta; |
224 |
> |
|
225 |
|
for( i=0; i<nAtoms; i++ ){ |
226 |
< |
atomIndex = i * 3; |
227 |
< |
|
228 |
< |
// velocity half step |
229 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
230 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
231 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
163 |
< |
- vel[j]*(chi+eta)); |
164 |
< |
|
226 |
> |
|
227 |
> |
atoms[i]->getVel( vel ); |
228 |
> |
|
229 |
> |
for (j=0; j < 3; j++) |
230 |
> |
oldVel[3*i + j] = vel[j]; |
231 |
> |
|
232 |
|
if( atoms[i]->isDirectional() ){ |
233 |
< |
|
233 |
> |
|
234 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
235 |
+ |
|
236 |
+ |
dAtom->getJ( ji ); |
237 |
+ |
|
238 |
+ |
for (j=0; j < 3; j++) |
239 |
+ |
oldJi[3*i + j] = ji[j]; |
240 |
+ |
|
241 |
+ |
} |
242 |
+ |
} |
243 |
+ |
|
244 |
+ |
// do the iteration: |
245 |
+ |
|
246 |
+ |
instVol = tStats->getVolume(); |
247 |
+ |
|
248 |
+ |
for (k=0; k < 4; k++) { |
249 |
+ |
|
250 |
+ |
instTemp = tStats->getTemperature(); |
251 |
+ |
instPress = tStats->getPressure(); |
252 |
+ |
|
253 |
+ |
// evolve chi another half step using the temperature at t + dt/2 |
254 |
+ |
|
255 |
+ |
prevChi = chi; |
256 |
+ |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
257 |
+ |
(tauThermostat*tauThermostat); |
258 |
+ |
|
259 |
+ |
preEta = eta; |
260 |
+ |
eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / |
261 |
+ |
(p_convert*NkBT*tb2)); |
262 |
+ |
|
263 |
+ |
|
264 |
+ |
for( i=0; i<nAtoms; i++ ){ |
265 |
+ |
|
266 |
+ |
atoms[i]->getFrc( frc ); |
267 |
+ |
atoms[i]->getVel(vel); |
268 |
|
|
269 |
< |
// get and convert the torque to body frame |
269 |
> |
mass = atoms[i]->getMass(); |
270 |
|
|
271 |
< |
Tb[0] = dAtom->getTx(); |
272 |
< |
Tb[1] = dAtom->getTy(); |
273 |
< |
Tb[2] = dAtom->getTz(); |
271 |
> |
// velocity half step |
272 |
> |
for (j=0; j < 3; j++) |
273 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta)); |
274 |
|
|
275 |
< |
dAtom->lab2Body( Tb ); |
275 |
> |
atoms[i]->setVel( vel ); |
276 |
|
|
277 |
< |
// get the angular momentum, and complete the angular momentum |
278 |
< |
// half step |
277 |
> |
if( atoms[i]->isDirectional() ){ |
278 |
> |
|
279 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
280 |
> |
|
281 |
> |
// get and convert the torque to body frame |
282 |
> |
|
283 |
> |
dAtom->getTrq( Tb ); |
284 |
> |
dAtom->lab2Body( Tb ); |
285 |
> |
|
286 |
> |
for (j=0; j < 3; j++) |
287 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
288 |
|
|
289 |
< |
ji[0] = dAtom->getJx(); |
290 |
< |
ji[1] = dAtom->getJy(); |
182 |
< |
ji[2] = dAtom->getJz(); |
183 |
< |
|
184 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
185 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
186 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
187 |
< |
|
188 |
< |
dAtom->setJx( ji[0] ); |
189 |
< |
dAtom->setJy( ji[1] ); |
190 |
< |
dAtom->setJz( ji[2] ); |
289 |
> |
dAtom->setJ( ji ); |
290 |
> |
} |
291 |
|
} |
292 |
+ |
|
293 |
+ |
if (nConstrained){ |
294 |
+ |
constrainB(); |
295 |
+ |
} |
296 |
+ |
|
297 |
+ |
if (fabs(prevChi - chi) <= |
298 |
+ |
chiTolerance && fabs(preEta -eta) <= etaTolerance) |
299 |
+ |
break; |
300 |
|
} |
301 |
+ |
|
302 |
+ |
//calculate integral of chida |
303 |
+ |
integralOfChidt += dt2*chi; |
304 |
+ |
|
305 |
+ |
|
306 |
|
} |
307 |
|
|
308 |
< |
int NPTi::readyCheck() { |
308 |
> |
template<typename T> void NPTi<T>::resetIntegrator() { |
309 |
> |
chi = 0.0; |
310 |
> |
eta = 0.0; |
311 |
> |
} |
312 |
> |
|
313 |
> |
template<typename T> int NPTi<T>::readyCheck() { |
314 |
> |
|
315 |
> |
//check parent's readyCheck() first |
316 |
> |
if (T::readyCheck() == -1) |
317 |
> |
return -1; |
318 |
|
|
319 |
|
// First check to see if we have a target temperature. |
320 |
|
// Not having one is fatal. |
361 |
|
return -1; |
362 |
|
} |
363 |
|
|
364 |
+ |
if (!have_chi_tolerance) { |
365 |
+ |
sprintf( painCave.errMsg, |
366 |
+ |
"NPTi warning: setting chi tolerance to 1e-6\n"); |
367 |
+ |
chiTolerance = 1e-6; |
368 |
+ |
have_chi_tolerance = 1; |
369 |
+ |
painCave.isFatal = 0; |
370 |
+ |
simError(); |
371 |
+ |
} |
372 |
+ |
|
373 |
+ |
if (!have_eta_tolerance) { |
374 |
+ |
sprintf( painCave.errMsg, |
375 |
+ |
"NPTi warning: setting eta tolerance to 1e-6\n"); |
376 |
+ |
etaTolerance = 1e-6; |
377 |
+ |
have_eta_tolerance = 1; |
378 |
+ |
painCave.isFatal = 0; |
379 |
+ |
simError(); |
380 |
+ |
} |
381 |
|
// We need NkBT a lot, so just set it here: |
382 |
|
|
383 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
383 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
384 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
385 |
|
|
386 |
|
return 1; |
387 |
|
} |
388 |
+ |
|
389 |
+ |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
390 |
+ |
|
391 |
+ |
double conservedQuantity; |
392 |
+ |
double LkBT; |
393 |
+ |
double fkBT; |
394 |
+ |
double f1kBT; |
395 |
+ |
double f2kBT; |
396 |
+ |
double NkBT; |
397 |
+ |
double Energy; |
398 |
+ |
double thermostat_kinetic; |
399 |
+ |
double thermostat_potential; |
400 |
+ |
double barostat_kinetic; |
401 |
+ |
double barostat_potential; |
402 |
+ |
double tb2; |
403 |
+ |
double eta2; |
404 |
+ |
|
405 |
+ |
LkBT = (double)(info->getNDF() + 4) * kB * targetTemp; // 3N + 1 |
406 |
+ |
fkBT = (double)(info->getNDF() ) * kB * targetTemp; // 3N - 3 |
407 |
+ |
f1kBT = (double)(info->getNDF()+ 1) * kB * targetTemp; // 3N - 3 + 1 |
408 |
+ |
NkBT = (double)(info->getNDF() + 3) * kB * targetTemp; // 3N |
409 |
+ |
f2kBT = (double)(info->getNDF()+ 2) * kB * targetTemp; // 3N - 3 + 1 |
410 |
+ |
|
411 |
+ |
Energy = tStats->getTotalE(); |
412 |
+ |
|
413 |
+ |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
414 |
+ |
(2.0 * eConvert); |
415 |
+ |
|
416 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
417 |
+ |
|
418 |
+ |
|
419 |
+ |
barostat_kinetic = fkBT * tauBarostat * tauBarostat * eta * eta / |
420 |
+ |
(2.0 * eConvert); |
421 |
+ |
|
422 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
423 |
+ |
eConvert; |
424 |
+ |
|
425 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
426 |
+ |
barostat_kinetic + barostat_potential; |
427 |
+ |
|
428 |
+ |
cout.width(8); |
429 |
+ |
cout.precision(8); |
430 |
+ |
|
431 |
+ |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
432 |
+ |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
433 |
+ |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
434 |
+ |
|
435 |
+ |
return conservedQuantity; |
436 |
+ |
} |