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#include <cmath> |
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#include <math.h> |
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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 "mpiSimulation.hpp" |
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#endif |
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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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template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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T( 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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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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oldEta = 0.0; |
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} |
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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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//nothing for now |
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} |
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|
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template<typename T> void NPTi<T>::moveA() { |
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template<typename T> void NPTi<T>::resetIntegrator() { |
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eta = 0.0; |
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T::resetIntegrator(); |
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} |
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// int i, j; |
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// DirectionalAtom* dAtom; |
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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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template<typename T> void NPTi<T>::evolveEtaA() { |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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oldEta = eta; |
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} |
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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, scaleFactor; |
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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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template<typename T> void NPTi<T>::evolveEtaB() { |
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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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prevEta = eta; |
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eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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} |
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|
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// integralOfChidt += dt2* chi; |
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template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) { |
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int i; |
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|
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// for( i=0; i<nAtoms; i++ ){ |
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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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for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta ); |
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} |
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|
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// mass = atoms[i]->getMass(); |
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template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){ |
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int i; |
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|
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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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for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta ); |
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} |
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|
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// atoms[i]->setVel( vel ); |
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|
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// info->wrapVector(rj); |
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template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]){ |
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int j; |
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|
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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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for(j=0; j<3; j++) |
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sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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|
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// atoms[i]->setPos( pos ); |
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for(j=0; j<3; j++) |
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sc[j] *= eta; |
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} |
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|
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// if( atoms[i]->isDirectional() ){ |
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template<typename T> void NPTi<T>::scaleSimBox( void ){ |
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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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// 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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double scaleFactor; |
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|
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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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// // 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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// 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] / I[0][0]; |
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// this->rotate( 1, 2, angle, ji, A ); |
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|
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// // rotate about the y-axis |
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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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|
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// // rotate about the z-axis |
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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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|
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// // rotate about the y-axis |
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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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|
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// // rotate about the x-axis |
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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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|
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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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// } |
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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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// scaleFactor = exp(dt*eta); |
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|
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// if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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// sprintf( painCave.errMsg, |
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// "NPTi error: Attempting a Box scaling of more than 10 percent" |
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// " check your tauBarostat, as it is probably too small!\n" |
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// " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
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// ); |
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// painCave.isFatal = 1; |
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// simError(); |
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// } else { |
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// info->scaleBox(exp(dt*eta)); |
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// } |
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|
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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], 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, 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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|
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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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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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|
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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|
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mass = atoms[i]->getMass(); |
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|
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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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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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// get and convert the torque to body frame |
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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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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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// 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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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] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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|
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// rotate about the y-axis |
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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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|
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// rotate about the z-axis |
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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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|
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// rotate about the y-axis |
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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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|
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// rotate about the x-axis |
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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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|
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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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|
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// evolve chi and eta half step |
| 259 |
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|
| 260 |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 261 |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
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|
| 263 |
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//calculate the integral of chidt |
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integralOfChidt += dt2*chi; |
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|
| 266 |
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//save the old positions |
| 267 |
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for(i = 0; i < nAtoms; i++){ |
| 268 |
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atoms[i]->getPos(pos); |
| 269 |
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for(j = 0; j < 3; j++) |
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oldPos[i*3 + j] = pos[j]; |
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} |
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|
| 273 |
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//the first estimation of r(t+dt) is equal to r(t) |
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|
| 275 |
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for(k = 0; k < 4; k ++){ |
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|
| 277 |
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for(i =0 ; i < nAtoms; i++){ |
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|
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atoms[i]->getVel(vel); |
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atoms[i]->getPos(pos); |
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|
| 282 |
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for(j = 0; j < 3; j++) |
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rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
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|
| 285 |
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|
| 286 |
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//wrapVector(r(t)) = r(t)-R0 |
| 287 |
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//info->wrapVector(rj); |
| 288 |
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|
| 289 |
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for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
| 291 |
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|
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atoms[i]->setPos( pos ); |
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|
| 294 |
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} |
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|
| 296 |
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} |
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|
| 298 |
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|
| 299 |
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// Scale the box after all the positions have been moved: |
| 300 |
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|
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scaleFactor = exp(dt*eta); |
| 84 |
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|
| 85 |
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
| 94 |
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info->scaleBox(scaleFactor); |
| 95 |
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} |
| 96 |
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|
| 315 |
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//advance volume; |
| 316 |
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volume = volume * exp(dt*eta); |
| 97 |
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} |
| 98 |
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|
| 99 |
< |
template<typename T> void NPTi<T>::moveB( void ){ |
| 320 |
< |
|
| 321 |
< |
/* |
| 322 |
< |
int i, j; |
| 323 |
< |
DirectionalAtom* dAtom; |
| 324 |
< |
double Tb[3], ji[3]; |
| 325 |
< |
double vel[3], frc[3]; |
| 326 |
< |
double mass; |
| 327 |
< |
|
| 328 |
< |
double instaTemp, instaPress, instaVol; |
| 329 |
< |
double tt2, tb2; |
| 330 |
< |
|
| 331 |
< |
tt2 = tauThermostat * tauThermostat; |
| 332 |
< |
tb2 = tauBarostat * tauBarostat; |
| 333 |
< |
|
| 334 |
< |
instaTemp = tStats->getTemperature(); |
| 335 |
< |
instaPress = tStats->getPressure(); |
| 336 |
< |
instaVol = tStats->getVolume(); |
| 337 |
< |
|
| 338 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 339 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
| 340 |
< |
(p_convert*NkBT*tb2)); |
| 341 |
< |
integralOfChidt += dt2*chi; |
| 342 |
< |
|
| 343 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 99 |
> |
template<typename T> bool NPTi<T>::etaConverged() { |
| 100 |
|
|
| 101 |
< |
atoms[i]->getVel( vel ); |
| 346 |
< |
atoms[i]->getFrc( frc ); |
| 347 |
< |
|
| 348 |
< |
mass = atoms[i]->getMass(); |
| 349 |
< |
|
| 350 |
< |
// velocity half step |
| 351 |
< |
for (j=0; j < 3; j++) |
| 352 |
< |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
| 353 |
< |
|
| 354 |
< |
atoms[i]->setVel( vel ); |
| 355 |
< |
|
| 356 |
< |
if( atoms[i]->isDirectional() ){ |
| 357 |
< |
|
| 358 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 359 |
< |
|
| 360 |
< |
// get and convert the torque to body frame |
| 361 |
< |
|
| 362 |
< |
dAtom->getTrq( Tb ); |
| 363 |
< |
dAtom->lab2Body( Tb ); |
| 364 |
< |
|
| 365 |
< |
// get the angular momentum, and propagate a half step |
| 366 |
< |
|
| 367 |
< |
dAtom->getJ( ji ); |
| 368 |
< |
|
| 369 |
< |
for (j=0; j < 3; j++) |
| 370 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 371 |
< |
|
| 372 |
< |
dAtom->setJ( ji ); |
| 373 |
< |
} |
| 374 |
< |
} |
| 375 |
< |
|
| 376 |
< |
*/ |
| 377 |
< |
|
| 378 |
< |
//new version of NPTi |
| 379 |
< |
int i, j, k; |
| 380 |
< |
DirectionalAtom* dAtom; |
| 381 |
< |
double Tb[3], ji[3]; |
| 382 |
< |
double vel[3], frc[3]; |
| 383 |
< |
double mass; |
| 384 |
< |
|
| 385 |
< |
double instTemp, instPress, instVol; |
| 386 |
< |
double tt2, tb2; |
| 387 |
< |
double oldChi, prevChi; |
| 388 |
< |
double oldEta, preEta; |
| 389 |
< |
|
| 390 |
< |
tt2 = tauThermostat * tauThermostat; |
| 391 |
< |
tb2 = tauBarostat * tauBarostat; |
| 392 |
< |
|
| 393 |
< |
|
| 394 |
< |
// Set things up for the iteration: |
| 395 |
< |
|
| 396 |
< |
oldChi = chi; |
| 397 |
< |
oldEta = eta; |
| 398 |
< |
|
| 399 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 400 |
< |
|
| 401 |
< |
atoms[i]->getVel( vel ); |
| 402 |
< |
|
| 403 |
< |
for (j=0; j < 3; j++) |
| 404 |
< |
oldVel[3*i + j] = vel[j]; |
| 405 |
< |
|
| 406 |
< |
if( atoms[i]->isDirectional() ){ |
| 407 |
< |
|
| 408 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 409 |
< |
|
| 410 |
< |
dAtom->getJ( ji ); |
| 411 |
< |
|
| 412 |
< |
for (j=0; j < 3; j++) |
| 413 |
< |
oldJi[3*i + j] = ji[j]; |
| 414 |
< |
|
| 415 |
< |
} |
| 416 |
< |
} |
| 417 |
< |
|
| 418 |
< |
// do the iteration: |
| 419 |
< |
|
| 420 |
< |
instVol = tStats->getVolume(); |
| 421 |
< |
|
| 422 |
< |
for (k=0; k < 4; k++) { |
| 423 |
< |
|
| 424 |
< |
instTemp = tStats->getTemperature(); |
| 425 |
< |
instPress = tStats->getPressure(); |
| 426 |
< |
|
| 427 |
< |
// evolve chi another half step using the temperature at t + dt/2 |
| 428 |
< |
|
| 429 |
< |
prevChi = chi; |
| 430 |
< |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
| 431 |
< |
(tauThermostat*tauThermostat); |
| 432 |
< |
|
| 433 |
< |
preEta = eta; |
| 434 |
< |
eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / |
| 435 |
< |
(p_convert*NkBT*tb2)); |
| 436 |
< |
|
| 437 |
< |
|
| 438 |
< |
for( i=0; i<nAtoms; i++ ){ |
| 439 |
< |
|
| 440 |
< |
atoms[i]->getFrc( frc ); |
| 441 |
< |
atoms[i]->getVel(vel); |
| 442 |
< |
|
| 443 |
< |
mass = atoms[i]->getMass(); |
| 444 |
< |
|
| 445 |
< |
// velocity half step |
| 446 |
< |
for (j=0; j < 3; j++) |
| 447 |
< |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta)); |
| 448 |
< |
|
| 449 |
< |
atoms[i]->setVel( vel ); |
| 450 |
< |
|
| 451 |
< |
if( atoms[i]->isDirectional() ){ |
| 452 |
< |
|
| 453 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 454 |
< |
|
| 455 |
< |
// get and convert the torque to body frame |
| 456 |
< |
|
| 457 |
< |
dAtom->getTrq( Tb ); |
| 458 |
< |
dAtom->lab2Body( Tb ); |
| 459 |
< |
|
| 460 |
< |
for (j=0; j < 3; j++) |
| 461 |
< |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 462 |
< |
|
| 463 |
< |
dAtom->setJ( ji ); |
| 464 |
< |
} |
| 465 |
< |
} |
| 466 |
< |
|
| 467 |
< |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
| 468 |
< |
break; |
| 469 |
< |
} |
| 470 |
< |
|
| 471 |
< |
//calculate integral of chida |
| 472 |
< |
integralOfChidt += dt2*chi; |
| 473 |
< |
|
| 474 |
< |
|
| 101 |
> |
return ( fabs(prevEta - eta) <= etaTolerance ); |
| 102 |
|
} |
| 103 |
|
|
| 477 |
– |
template<typename T> void NPTi<T>::resetIntegrator() { |
| 478 |
– |
chi = 0.0; |
| 479 |
– |
eta = 0.0; |
| 480 |
– |
} |
| 481 |
– |
|
| 482 |
– |
template<typename T> int NPTi<T>::readyCheck() { |
| 483 |
– |
|
| 484 |
– |
//check parent's readyCheck() first |
| 485 |
– |
if (T::readyCheck() == -1) |
| 486 |
– |
return -1; |
| 487 |
– |
|
| 488 |
– |
// First check to see if we have a target temperature. |
| 489 |
– |
// Not having one is fatal. |
| 490 |
– |
|
| 491 |
– |
if (!have_target_temp) { |
| 492 |
– |
sprintf( painCave.errMsg, |
| 493 |
– |
"NPTi error: You can't use the NPTi integrator\n" |
| 494 |
– |
" without a targetTemp!\n" |
| 495 |
– |
); |
| 496 |
– |
painCave.isFatal = 1; |
| 497 |
– |
simError(); |
| 498 |
– |
return -1; |
| 499 |
– |
} |
| 500 |
– |
|
| 501 |
– |
if (!have_target_pressure) { |
| 502 |
– |
sprintf( painCave.errMsg, |
| 503 |
– |
"NPTi error: You can't use the NPTi integrator\n" |
| 504 |
– |
" without a targetPressure!\n" |
| 505 |
– |
); |
| 506 |
– |
painCave.isFatal = 1; |
| 507 |
– |
simError(); |
| 508 |
– |
return -1; |
| 509 |
– |
} |
| 510 |
– |
|
| 511 |
– |
// We must set tauThermostat. |
| 512 |
– |
|
| 513 |
– |
if (!have_tau_thermostat) { |
| 514 |
– |
sprintf( painCave.errMsg, |
| 515 |
– |
"NPTi error: If you use the NPTi\n" |
| 516 |
– |
" integrator, you must set tauThermostat.\n"); |
| 517 |
– |
painCave.isFatal = 1; |
| 518 |
– |
simError(); |
| 519 |
– |
return -1; |
| 520 |
– |
} |
| 521 |
– |
|
| 522 |
– |
// We must set tauBarostat. |
| 523 |
– |
|
| 524 |
– |
if (!have_tau_barostat) { |
| 525 |
– |
sprintf( painCave.errMsg, |
| 526 |
– |
"NPTi error: If you use the NPTi\n" |
| 527 |
– |
" integrator, you must set tauBarostat.\n"); |
| 528 |
– |
painCave.isFatal = 1; |
| 529 |
– |
simError(); |
| 530 |
– |
return -1; |
| 531 |
– |
} |
| 532 |
– |
|
| 533 |
– |
if (!have_chi_tolerance) { |
| 534 |
– |
sprintf( painCave.errMsg, |
| 535 |
– |
"NPTi warning: setting chi tolerance to 1e-6\n"); |
| 536 |
– |
chiTolerance = 1e-6; |
| 537 |
– |
have_chi_tolerance = 1; |
| 538 |
– |
painCave.isFatal = 0; |
| 539 |
– |
simError(); |
| 540 |
– |
} |
| 541 |
– |
|
| 542 |
– |
if (!have_eta_tolerance) { |
| 543 |
– |
sprintf( painCave.errMsg, |
| 544 |
– |
"NPTi warning: setting eta tolerance to 1e-6\n"); |
| 545 |
– |
etaTolerance = 1e-6; |
| 546 |
– |
have_eta_tolerance = 1; |
| 547 |
– |
painCave.isFatal = 0; |
| 548 |
– |
simError(); |
| 549 |
– |
} |
| 550 |
– |
// We need NkBT a lot, so just set it here: |
| 551 |
– |
|
| 552 |
– |
NkBT = (double)Nparticles * kB * targetTemp; |
| 553 |
– |
fkBT = (double)info->ndf * kB * targetTemp; |
| 554 |
– |
|
| 555 |
– |
return 1; |
| 556 |
– |
} |
| 557 |
– |
|
| 104 |
|
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
| 105 |
|
|
| 106 |
|
double conservedQuantity; |
| 107 |
< |
double tb2; |
| 108 |
< |
double eta2; |
| 109 |
< |
double E_NPT; |
| 110 |
< |
double U; |
| 111 |
< |
double TS; |
| 112 |
< |
double PV; |
| 113 |
< |
double extra; |
| 107 |
> |
double Energy; |
| 108 |
> |
double thermostat_kinetic; |
| 109 |
> |
double thermostat_potential; |
| 110 |
> |
double barostat_kinetic; |
| 111 |
> |
double barostat_potential; |
| 112 |
> |
|
| 113 |
> |
Energy = tStats->getTotalE(); |
| 114 |
|
|
| 115 |
< |
static double pre_U; |
| 116 |
< |
static double pre_TS; |
| 571 |
< |
static double pre_PV; |
| 572 |
< |
static double pre_extra; |
| 573 |
< |
static int hackCount = 0; |
| 115 |
> |
thermostat_kinetic = fkBT* tt2 * chi * chi / |
| 116 |
> |
(2.0 * eConvert); |
| 117 |
|
|
| 118 |
< |
double delta_U; |
| 576 |
< |
double delta_TS; |
| 577 |
< |
double delta_PV; |
| 578 |
< |
double delta_extra; |
| 118 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 119 |
|
|
| 580 |
– |
U = tStats->getTotalE(); |
| 120 |
|
|
| 121 |
< |
TS = fkBT * |
| 122 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 121 |
> |
barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta / |
| 122 |
> |
(2.0 * eConvert); |
| 123 |
> |
|
| 124 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 125 |
> |
eConvert; |
| 126 |
|
|
| 127 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 128 |
< |
|
| 587 |
< |
tb2 = tauBarostat * tauBarostat; |
| 588 |
< |
eta2 = eta * eta; |
| 589 |
< |
|
| 590 |
< |
extra = (fkBT * tb2 * eta2 / 2.0 ) / eConvert; |
| 591 |
< |
/* |
| 592 |
< |
if(hackCount == 0){ |
| 593 |
< |
pre_U = U; |
| 594 |
< |
pre_TS =TS; |
| 595 |
< |
pre_PV = PV; |
| 596 |
< |
pre_extra =extra; |
| 597 |
< |
hackCount ++; |
| 598 |
< |
} |
| 599 |
< |
|
| 600 |
< |
delta_U = U - pre_U; |
| 601 |
< |
delta_TS = TS - pre_TS; |
| 602 |
< |
delta_PV = PV - pre_PV; |
| 603 |
< |
delta_extra = extra - pre_extra; |
| 604 |
< |
*/ |
| 605 |
< |
cout.width(8); |
| 606 |
< |
cout.precision(8); |
| 607 |
< |
|
| 127 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 128 |
> |
barostat_kinetic + barostat_potential; |
| 129 |
|
|
| 130 |
< |
cout << info->getTime() << "\t" |
| 131 |
< |
<< chi << "\t" |
| 611 |
< |
<< eta << "\t" |
| 612 |
< |
<< U << "\t" |
| 613 |
< |
<< TS << "\t" |
| 614 |
< |
<< PV << "\t" |
| 615 |
< |
<< extra << "\t" |
| 616 |
< |
<< U+TS+PV+extra << endl; |
| 130 |
> |
// cout.width(8); |
| 131 |
> |
// cout.precision(8); |
| 132 |
|
|
| 133 |
< |
/* |
| 134 |
< |
pre_U = U; |
| 135 |
< |
pre_TS =TS; |
| 621 |
< |
pre_PV = PV; |
| 622 |
< |
pre_extra =extra; |
| 623 |
< |
|
| 624 |
< |
|
| 625 |
< |
cout << info->getTime() << "\t" |
| 626 |
< |
<< U << "\t" |
| 627 |
< |
<< U+TS << "\t" |
| 628 |
< |
<< U+TS+PV << "\t" |
| 629 |
< |
<< U+TS+PV+extra << endl; |
| 630 |
< |
*/ |
| 631 |
< |
conservedQuantity = U+TS+PV+extra; |
| 133 |
> |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 134 |
> |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 135 |
> |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 136 |
|
return conservedQuantity; |
| 137 |
|
} |