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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 "NVT.hpp" |
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|
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#include "simError.h" |
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|
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|
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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|
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NVT::NVT() { |
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zeta = 0.0; |
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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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chi = 0.0; |
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have_tau_thermostat = 0; |
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have_target_temp = 0; |
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have_qmass = 0; |
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have_chi_tolerance = 0; |
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integralOfChidt = 0.0; |
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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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void NVT::moveA() { |
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template<typename T> NVT<T>::~NVT() { |
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delete[] oldVel; |
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delete[] oldJi; |
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} |
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|
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template<typename T> void NVT<T>::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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int i, j; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double Tb[3], ji[3]; |
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double mass; |
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double vel[3], pos[3], frc[3]; |
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|
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ke = tStats->getKinetic() * eConvert; |
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zeta += dt2 * ( (2.0 * ke - NkBT) / qmass ); |
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double instTemp; |
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|
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// We need the temperature at time = t for the chi update below: |
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|
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instTemp = tStats->getTemperature(); |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta); |
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|
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// position whole step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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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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|
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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); |
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// position whole step |
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pos[j] += dt * vel[j]; |
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} |
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|
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atoms[i]->setVel( vel ); |
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atoms[i]->setPos( pos ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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|
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// get and convert the torque to body frame |
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|
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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|
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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|
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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dAtom->getJ( ji ); |
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|
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta); |
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this->rotationPropagation( dAtom, ji ); |
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|
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
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|
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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
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|
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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} |
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|
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dAtom->setJ( ji ); |
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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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|
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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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|
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chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
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integralOfChidt += chi*dt2; |
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|
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} |
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|
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void Integrator::moveB( void ){ |
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int i,j,k; |
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int atomIndex; |
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template<typename T> void NVT<T>::moveB( void ){ |
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int i, j, k; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double Tb[3], ji[3]; |
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double vel[3], frc[3]; |
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double mass; |
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double instTemp; |
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double oldChi, prevChi; |
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|
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ke = tStats->getKinetic() * eConvert; |
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zeta += dt2 * ( (2.0 * ke - NkBT) / qmass ); |
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|
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// Set things up for the iteration: |
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|
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oldChi = chi; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta); |
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|
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|
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atoms[i]->getVel( vel ); |
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|
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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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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oldJi[3*i + j] = ji[j]; |
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|
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} |
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} |
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|
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// do the iteration: |
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|
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for (k=0; k < 4; k++) { |
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|
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instTemp = tStats->getTemperature(); |
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|
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// evolve chi another half step using the temperature at t + dt/2 |
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|
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prevChi = chi; |
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chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
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(tauThermostat*tauThermostat); |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getFrc( frc ); |
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atoms[i]->getVel(vel); |
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|
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// get and convert the torque to body frame |
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mass = atoms[i]->getMass(); |
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|
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Tb[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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// velocity half step |
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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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|
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dAtom->lab2Body( Tb ); |
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atoms[i]->setVel( vel ); |
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|
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// get the angular momentum, and complete the angular momentum |
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// half step |
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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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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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|
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ji[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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|
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta); |
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|
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jx2 = ji[0] * ji[0]; |
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jy2 = ji[1] * ji[1]; |
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jz2 = ji[2] * ji[2]; |
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|
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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dAtom->setJ( ji ); |
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} |
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} |
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|
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if (nConstrained){ |
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constrainB(); |
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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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|
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integralOfChidt += dt2*chi; |
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} |
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|
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int NVT::readyCheck() { |
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double NkBT; |
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template<typename T> void NVT<T>::resetIntegrator( void ){ |
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|
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chi = 0.0; |
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integralOfChidt = 0.0; |
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} |
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|
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template<typename T> int NVT<T>::readyCheck() { |
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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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|
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// First check to see if we have a target temperature. |
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// Not having one is fatal. |
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|
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simError(); |
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return -1; |
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} |
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|
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// Next check to see that we have a reasonable number of degrees of freedom |
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// and then set NkBT if we do have it. Unreasonable numbers of DOFs |
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// are also fatal. |
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|
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if (entry_plug->ndf > 0) { |
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NkBT = (double)entry_plug->ndf * kB * targetTemp; |
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} else { |
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|
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// We must set tauThermostat. |
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|
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if (!have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NVT error: We got a silly number of degrees of freedom!\n" |
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); |
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"NVT error: If you use the constant temperature\n" |
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" integrator, you must set tauThermostat.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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return -1; |
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} |
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|
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// We have our choice on setting qmass or tauThermostat. One of them |
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// must be set. |
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} |
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|
|
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if (!have_qmass) { |
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if (have_tau_thermostat) { |
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sprintf( painCave.errMsg, |
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"NVT info: Setting qMass = %d\n", tauThermostat * NkBT); |
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this->setQmass(tauThermostat * NkBT); |
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painCave.isFatal = 0; |
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simError(); |
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} else { |
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sprintf( painCave.errMsg, |
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"NVT error: If you use the constant temperature\n" |
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" integrator, you must set either tauThermostat or qMass.\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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|
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return 1; |
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if (!have_chi_tolerance) { |
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> |
sprintf( painCave.errMsg, |
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"NVT warning: setting chi tolerance to 1e-6\n"); |
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> |
chiTolerance = 1e-6; |
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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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|
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} |
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|
|
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< |
#endif |
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> |
template<typename T> double NVT<T>::getConservedQuantity(void){ |
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> |
|
231 |
> |
double conservedQuantity; |
232 |
> |
double fkBT; |
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> |
double Energy; |
234 |
> |
double thermostat_kinetic; |
235 |
> |
double thermostat_potential; |
236 |
> |
|
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> |
fkBT = (double)(info->getNDF() ) * kB * targetTemp; |
238 |
> |
|
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> |
Energy = tStats->getTotalE(); |
240 |
> |
|
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> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
242 |
> |
(2.0 * eConvert); |
243 |
> |
|
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> |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
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> |
|
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> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
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> |
|
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> |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
249 |
> |
"\t" << thermostat_potential << "\t" << conservedQuantity << endl; |
250 |
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|
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> |
return conservedQuantity; |
252 |
> |
} |