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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 "SimInfo.hpp" |
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#include "ForceFields.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 "NVT.hpp" |
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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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have_tau_thermostat = 0; |
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have_target_temp = 0; |
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have_qmass = 0; |
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} |
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|
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void NVT::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[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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|
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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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pos[j] += dt * vel[j]; |
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|
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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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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->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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|
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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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// 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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} |
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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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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[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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|
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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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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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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->lab2Body( Tb ); |
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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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|
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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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} |
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} |
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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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|
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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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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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); |
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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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// 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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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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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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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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} |
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|
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#endif |
