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#include <cmath> |
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#include <iostream> |
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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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// 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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NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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NPT( theInfo, the_ff ) |
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{ |
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chi = 0.0; |
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GenericData* data; |
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double *etaArray; |
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int test; |
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eta = 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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oldEta = 0.0; |
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|
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// retrieve eta array from simInfo if it exists |
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data = info->getProperty(ETAVALUE_ID); |
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if(data != NULL){ |
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|
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test = data->getDarray(etaArray); |
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if( test == 9 ){ |
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eta = etaArray[0]; |
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delete[] etaArray; |
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} |
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else |
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std::cerr << "NPTi error: etaArray is not length 9 (actual = " << test |
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<< ").\n" |
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<< " Simulation wil proceed with eta = 0;\n"; |
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} |
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} |
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template<typename T> void NPTi<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 vel[3], pos[3], frc[3]; |
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NPTi::~NPTi() { |
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//nothing for now |
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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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void NPTi::resetIntegrator() { |
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eta = 0.0; |
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NPT::resetIntegrator(); |
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} |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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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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// first evolve chi a half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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void NPTi::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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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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void NPTi::evolveEtaB() { |
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mass = atoms[i]->getMass(); |
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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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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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void NPTi::getVelScaleA(double sc[3], double vel[3]) { |
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int i; |
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atoms[i]->setVel( vel ); |
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for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta ); |
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} |
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info->wrapVector(rj); |
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void NPTi::getVelScaleB(double sc[3], int index ){ |
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int i; |
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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(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta ); |
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} |
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atoms[i]->setPos( pos ); |
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if( atoms[i]->isDirectional() ){ |
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void NPTi::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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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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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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dAtom->getJ( ji ); |
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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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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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void NPTi::scaleSimBox( void ){ |
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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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double scaleFactor; |
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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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// Scale the box after all the positions have been moved: |
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scaleFactor = exp(dt*eta); |
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if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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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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} else { |
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info->scaleBox(scaleFactor); |
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} |
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} |
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template<typename T> void NPTi<T>::moveB( void ){ |
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bool NPTi::etaConverged() { |
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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 vel[3], frc[3]; |
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double mass; |
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return ( fabs(prevEta - eta) <= etaTolerance ); |
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} |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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double NPTi::getConservedQuantity(void){ |
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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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double conservedQuantity; |
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double Energy; |
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double thermostat_kinetic; |
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double thermostat_potential; |
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double barostat_kinetic; |
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double barostat_potential; |
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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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for( i=0; i<nAtoms; i++ ){ |
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Energy = tStats->getTotalE(); |
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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thermostat_kinetic = fkBT* tt2 * chi * chi / |
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(2.0 * eConvert); |
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mass = atoms[i]->getMass(); |
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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// velocity half step |
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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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atoms[i]->setVel( vel ); |
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if( atoms[i]->isDirectional() ){ |
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barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta / |
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(2.0 * eConvert); |
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dAtom = (DirectionalAtom *)atoms[i]; |
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barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
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eConvert; |
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// get and convert the torque to body frame |
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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|
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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// cout.width(8); |
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// cout.precision(8); |
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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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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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dAtom->setJ( ji ); |
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} |
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} |
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// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
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// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
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// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
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return conservedQuantity; |
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} |
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template<typename T> void NPTi<T>::resetIntegrator() { |
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chi = 0.0; |
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eta = 0.0; |
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} |
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char* NPTi::getAdditionalParameters(void){ |
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template<typename T> int NPTi<T>::readyCheck() { |
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sprintf(addParamBuffer, |
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"\t%G\t%G;" |
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"\t%G\t%0.0\t%0.0;" |
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"\t%0.0\t%G\t%0.0;" |
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"\t%0.0\t%0.0\t%G;", |
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chi, integralOfChidt, |
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eta, eta, eta |
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); |
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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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if (!have_target_temp) { |
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sprintf( painCave.errMsg, |
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"NPTi error: You can't use the NPTi integrator\n" |
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" 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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if (!have_target_pressure) { |
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sprintf( painCave.errMsg, |
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"NPTi error: You can't use the NPTi integrator\n" |
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" without a targetPressure!\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 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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"NPTi error: If you use the NPTi\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 must set tauBarostat. |
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|
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if (!have_tau_barostat) { |
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sprintf( painCave.errMsg, |
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"NPTi error: If you use the NPTi\n" |
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" integrator, you must set tauBarostat.\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 need NkBT a lot, so just set it here: |
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|
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NkBT = (double)info->ndf * kB * targetTemp; |
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|
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return 1; |
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return addParamBuffer; |
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} |
