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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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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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GenericData* data; |
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DoubleData * chiValue; |
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DoubleData * integralOfChidtValue; |
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chiValue = NULL; |
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integralOfChidtValue = NULL; |
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|
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chi = 0.0; |
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have_tau_thermostat = 0; |
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have_target_temp = 0; |
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have_chi_tolerance = 0; |
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integralOfChidt = 0.0; |
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if( theInfo->useInitXSstate ){ |
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// retrieve chi and integralOfChidt from simInfo |
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data = info->getProperty(CHIVALUE_ID); |
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if(data){ |
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chiValue = dynamic_cast<DoubleData*>(data); |
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} |
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data = info->getProperty(INTEGRALOFCHIDT_ID); |
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if(data){ |
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integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
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} |
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// chi and integralOfChidt should appear by pair |
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if(chiValue && integralOfChidtValue){ |
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chi = chiValue->getData(); |
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integralOfChidt = integralOfChidtValue->getData(); |
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} |
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} |
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oldVel = new double[3*nAtoms]; |
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oldJi = new double[3*nAtoms]; |
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} |
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} |
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template<typename T> void NVT<T>::moveA() { |
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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 mass; |
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double vel[3], pos[3], frc[3]; |
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double instTemp; |
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// We need the temperature at time = t for the chi update below: |
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instTemp = tStats->getTemperature(); |
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getVel( vel ); |
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atoms[i]->setVel( vel ); |
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atoms[i]->setPos( pos ); |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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// get and convert the torque to body frame |
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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dAtom->getJ( ji ); |
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for (j=0; j < 3; j++) |
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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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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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dAtom->getA(A); |
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dAtom->getI(I); |
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// rotate about the x-axis |
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angle = dt2 * ji[0] / I[0][0]; |
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this->rotate( 1, 2, angle, ji, A ); |
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this->rotationPropagation( dAtom, ji ); |
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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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// 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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// 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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// 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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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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if (nConstrained){ |
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constrainA(); |
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} |
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// Finally, evolve chi a half step (just like a velocity) using |
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// Finally, evolve chi a half step (just like a velocity) using |
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// temperature at time t, not time t+dt/2 |
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chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
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// do the iteration: |
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for (k=0; k < 4; k++) { |
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instTemp = tStats->getTemperature(); |
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// evolve chi another half step using the temperature at t + dt/2 |
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prevChi = chi; |
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chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
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chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
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(tauThermostat*tauThermostat); |
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getFrc( frc ); |
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atoms[i]->getVel(vel); |
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mass = atoms[i]->getMass(); |
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// velocity half step |
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for (j=0; j < 3; j++) |
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for (j=0; j < 3; j++) |
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi); |
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atoms[i]->setVel( vel ); |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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// get and convert the torque to body frame |
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// get and convert the torque to body frame |
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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for (j=0; j < 3; j++) |
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dAtom->lab2Body( Tb ); |
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for (j=0; j < 3; j++) |
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ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
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dAtom->setJ( ji ); |
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} |
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} |
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if (fabs(prevChi - chi) <= chiTolerance) break; |
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} |
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integralOfChidt += dt2*chi; |
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} |
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template<typename T> void NVT<T>::resetIntegrator( void ){ |
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chi = 0.0; |
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integralOfChidt = 0.0; |
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} |
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//check parent's readyCheck() first |
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if (T::readyCheck() == -1) |
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return -1; |
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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if (!have_target_temp) { |
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sprintf( painCave.errMsg, |
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"NVT error: You can't use the NVT integrator without a targetTemp!\n" |
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simError(); |
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return -1; |
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} |
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// We must set tauThermostat. |
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if (!have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NVT error: If you use the constant temperature\n" |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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} |
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if (!have_chi_tolerance) { |
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sprintf( painCave.errMsg, |
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have_chi_tolerance = 1; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} |
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return 1; |
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return 1; |
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} |
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template<typename T> double NVT<T>::getConservedQuantity(void){ |
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double conservedQuantity; |
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double E_NVT; |
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double fkBT; |
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double Energy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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//HNVE |
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conservedQuantity = tStats->getTotalE(); |
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//HNVE |
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E_NVT = (info->getNDF() * kB * targetTemp * |
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(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert; |
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fkBT = (double)(info->getNDF() ) * kB * targetTemp; |
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conservedQuantity += E_NVT; |
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Energy = tStats->getTotalE(); |
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//cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl; |
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thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
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(2.0 * eConvert); |
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return conservedQuantity; |
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thermostat_potential = fkBT * integralOfChidt / eConvert; |
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
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return conservedQuantity; |
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} |
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template<typename T> string NVT<T>::getAdditionalParameters(void){ |
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string parameters; |
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const int BUFFERSIZE = 2000; // size of the read buffer |
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char buffer[BUFFERSIZE]; |
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sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
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parameters += buffer; |
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return parameters; |
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} |
