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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 "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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#include "simError.h" |
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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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// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
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// Molec. Phys., 78, 533. |
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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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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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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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GenericData* data; |
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DoubleArrayData * etaValue; |
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vector<double> etaArray; |
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|
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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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oldEta = 0.0; |
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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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if( theInfo->useInitXSstate ){ |
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// retrieve eta from simInfo if |
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data = info->getProperty(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleArrayData*>(data); |
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|
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if(etaValue){ |
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etaArray = etaValue->getData(); |
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eta = etaArray[0]; |
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oldEta = eta; |
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} |
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} |
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} |
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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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|
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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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template<typename T> void NPTi<T>::evolveEtaB() { |
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|
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// tt2 = tauThermostat * tauThermostat; |
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// tb2 = tauBarostat * tauBarostat; |
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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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// 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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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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// integralOfChidt += dt2* chi; |
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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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// 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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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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// mass = atoms[i]->getMass(); |
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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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// 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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|
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// atoms[i]->setVel( vel ); |
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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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// info->wrapVector(rj); |
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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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// 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] *= eta; |
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} |
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|
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// atoms[i]->setPos( pos ); |
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template<typename T> void NPTi<T>::scaleSimBox( void ){ |
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|
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// if( atoms[i]->isDirectional() ){ |
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double scaleFactor; |
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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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|
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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 ); |
210 |
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|
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if( atoms[i]->isDirectional() ){ |
212 |
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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 |
229 |
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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); |
244 |
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|
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// rotate about the y-axis |
246 |
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angle = dt2 * ji[1] / I[1][1]; |
247 |
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this->rotate( 2, 0, angle, ji, A ); |
248 |
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|
249 |
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// rotate about the x-axis |
250 |
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angle = dt2 * ji[0] / I[0][0]; |
251 |
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this->rotate( 1, 2, angle, ji, A ); |
252 |
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|
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dAtom->setJ( ji ); |
254 |
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dAtom->setA( A ); |
255 |
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} |
256 |
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} |
257 |
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|
258 |
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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)); |
262 |
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|
263 |
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//calculate the integral of chidt |
264 |
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integralOfChidt += dt2*chi; |
265 |
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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++) |
270 |
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oldPos[i*3 + j] = pos[j]; |
271 |
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} |
272 |
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|
273 |
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//the first estimation of r(t+dt) is equal to r(t) |
274 |
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|
275 |
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for(k = 0; k < 4; k ++){ |
276 |
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|
277 |
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for(i =0 ; i < nAtoms; i++){ |
278 |
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|
279 |
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atoms[i]->getVel(vel); |
280 |
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atoms[i]->getPos(pos); |
281 |
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|
282 |
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for(j = 0; j < 3; j++) |
283 |
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rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
284 |
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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++) |
290 |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
291 |
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|
292 |
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atoms[i]->setPos( pos ); |
293 |
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|
294 |
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} |
295 |
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|
296 |
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} |
297 |
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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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|
101 |
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scaleFactor = exp(dt*eta); |
102 |
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|
103 |
|
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
108 |
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); |
109 |
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painCave.isFatal = 1; |
110 |
|
simError(); |
111 |
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} else { |
112 |
< |
info->scaleBox(scaleFactor); |
313 |
< |
} |
314 |
< |
|
315 |
< |
//advance volume; |
316 |
< |
volume = volume * exp(dt*eta); |
317 |
< |
} |
318 |
< |
|
319 |
< |
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++ ){ |
344 |
< |
|
345 |
< |
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 |
< |
} |
111 |
> |
} else { |
112 |
> |
info->scaleBox(scaleFactor); |
113 |
|
} |
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; |
114 |
|
|
115 |
< |
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; |
115 |
> |
} |
116 |
|
|
117 |
+ |
template<typename T> bool NPTi<T>::etaConverged() { |
118 |
|
|
119 |
< |
// Set things up for the iteration: |
119 |
> |
return ( fabs(prevEta - eta) <= etaTolerance ); |
120 |
> |
} |
121 |
|
|
122 |
< |
oldChi = chi; |
397 |
< |
oldEta = eta; |
122 |
> |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
123 |
|
|
124 |
< |
for( i=0; i<nAtoms; i++ ){ |
124 |
> |
double conservedQuantity; |
125 |
> |
double Energy; |
126 |
> |
double thermostat_kinetic; |
127 |
> |
double thermostat_potential; |
128 |
> |
double barostat_kinetic; |
129 |
> |
double barostat_potential; |
130 |
|
|
131 |
< |
atoms[i]->getVel( vel ); |
131 |
> |
Energy = tStats->getTotalE(); |
132 |
|
|
133 |
< |
for (j=0; j < 3; j++) |
134 |
< |
oldVel[3*i + j] = vel[j]; |
133 |
> |
thermostat_kinetic = fkBT* tt2 * chi * chi / |
134 |
> |
(2.0 * eConvert); |
135 |
|
|
136 |
< |
if( atoms[i]->isDirectional() ){ |
136 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
137 |
|
|
408 |
– |
dAtom = (DirectionalAtom *)atoms[i]; |
138 |
|
|
139 |
< |
dAtom->getJ( ji ); |
139 |
> |
barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta / |
140 |
> |
(2.0 * eConvert); |
141 |
|
|
142 |
< |
for (j=0; j < 3; j++) |
143 |
< |
oldJi[3*i + j] = ji[j]; |
142 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
143 |
> |
eConvert; |
144 |
|
|
145 |
< |
} |
146 |
< |
} |
145 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
146 |
> |
barostat_kinetic + barostat_potential; |
147 |
|
|
148 |
< |
// do the iteration: |
148 |
> |
// cout.width(8); |
149 |
> |
// cout.precision(8); |
150 |
|
|
151 |
< |
instVol = tStats->getVolume(); |
152 |
< |
|
153 |
< |
for (k=0; k < 4; k++) { |
154 |
< |
|
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 |
< |
|
151 |
> |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
152 |
> |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
153 |
> |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
154 |
> |
return conservedQuantity; |
155 |
|
} |
156 |
|
|
157 |
< |
template<typename T> void NPTi<T>::resetIntegrator() { |
158 |
< |
chi = 0.0; |
159 |
< |
eta = 0.0; |
160 |
< |
} |
157 |
> |
template<typename T> string NPTi<T>::getAdditionalParameters(void){ |
158 |
> |
string parameters; |
159 |
> |
const int BUFFERSIZE = 2000; // size of the read buffer |
160 |
> |
char buffer[BUFFERSIZE]; |
161 |
|
|
162 |
< |
template<typename T> int NPTi<T>::readyCheck() { |
162 |
> |
sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
163 |
> |
parameters += buffer; |
164 |
|
|
165 |
< |
//check parent's readyCheck() first |
166 |
< |
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 |
< |
} |
165 |
> |
sprintf(buffer,"\t%G\t0\t0;", eta); |
166 |
> |
parameters += buffer; |
167 |
|
|
168 |
< |
if (!have_target_pressure) { |
169 |
< |
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 |
< |
} |
168 |
> |
sprintf(buffer,"\t0\t%G\t0;", eta); |
169 |
> |
parameters += buffer; |
170 |
|
|
171 |
< |
// We must set tauBarostat. |
172 |
< |
|
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 |
< |
} |
171 |
> |
sprintf(buffer,"\t0\t0\t%G;", eta); |
172 |
> |
parameters += buffer; |
173 |
|
|
174 |
< |
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 |
< |
} |
174 |
> |
return parameters; |
175 |
|
|
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; |
176 |
|
} |
557 |
– |
|
558 |
– |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
559 |
– |
|
560 |
– |
double conservedQuantity; |
561 |
– |
double tb2; |
562 |
– |
double eta2; |
563 |
– |
double E_NPT; |
564 |
– |
double U; |
565 |
– |
double TS; |
566 |
– |
double PV; |
567 |
– |
double extra; |
568 |
– |
|
569 |
– |
static double pre_U; |
570 |
– |
static double pre_TS; |
571 |
– |
static double pre_PV; |
572 |
– |
static double pre_extra; |
573 |
– |
static int hackCount = 0; |
574 |
– |
|
575 |
– |
double delta_U; |
576 |
– |
double delta_TS; |
577 |
– |
double delta_PV; |
578 |
– |
double delta_extra; |
579 |
– |
|
580 |
– |
U = tStats->getTotalE(); |
581 |
– |
|
582 |
– |
TS = fkBT * |
583 |
– |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
584 |
– |
|
585 |
– |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
586 |
– |
|
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 |
– |
|
608 |
– |
|
609 |
– |
cout << info->getTime() << "\t" |
610 |
– |
<< chi << "\t" |
611 |
– |
<< eta << "\t" |
612 |
– |
<< U << "\t" |
613 |
– |
<< TS << "\t" |
614 |
– |
<< PV << "\t" |
615 |
– |
<< extra << "\t" |
616 |
– |
<< U+TS+PV+extra << endl; |
617 |
– |
|
618 |
– |
/* |
619 |
– |
pre_U = U; |
620 |
– |
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; |
632 |
– |
return conservedQuantity; |
633 |
– |
} |