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#include <cmath> |
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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 "simError.h" |
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|
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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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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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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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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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|
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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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} |
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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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} |
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|
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template<typename T> void NPTi<T>::moveA() { |
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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 |
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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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atoms[i]->setVel( vel ); |
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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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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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// advance chi half step |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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|
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// calculate the integral of chidt |
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|
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integralOfChidt += dt2*chi; |
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|
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// advance eta half step |
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|
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
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|
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//save the old positions |
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for(i = 0; i < nAtoms; i++){ |
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atoms[i]->getPos(pos); |
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for(j = 0; j < 3; j++) |
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oldPos[i*3 + j] = pos[j]; |
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} |
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|
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//the first estimation of r(t+dt) is equal to r(t) |
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|
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for(k = 0; k < 4; k ++){ |
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|
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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]->getPos(pos); |
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|
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for(j = 0; j < 3; j++) |
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rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
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|
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for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
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|
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atoms[i]->setPos( pos ); |
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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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|
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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(scaleFactor); |
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} |
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|
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} |
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|
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template<typename T> void NPTi<T>::moveB( void ){ |
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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 vel[3], frc[3]; |
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double mass; |
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|
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double oldChi, prevChi; |
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double oldEta, prevEta; |
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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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// Set things up for the iteration: |
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|
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oldChi = chi; |
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oldEta = eta; |
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|
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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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|
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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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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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instaVol = tStats->getVolume(); |
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|
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for (k=0; k < 4; k++) { |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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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 * ( instaTemp / targetTemp - 1.0) / tt2; |
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|
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prevEta = eta; |
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|
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// advance eta half step and calculate scale factor for velocity |
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|
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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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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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mass = atoms[i]->getMass(); |
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|
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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 + eta)); |
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|
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atoms[i]->setVel( vel ); |
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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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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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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) <= |
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chiTolerance && fabs(prevEta -eta) <= etaTolerance) |
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break; |
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} |
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|
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//calculate integral of chidt |
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integralOfChidt += dt2*chi; |
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|
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} |
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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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|
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template<typename T> int NPTi<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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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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if (!have_chi_tolerance) { |
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sprintf( painCave.errMsg, |
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"NPTi 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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if (!have_eta_tolerance) { |
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sprintf( painCave.errMsg, |
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"NPTi warning: setting eta tolerance to 1e-6\n"); |
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etaTolerance = 1e-6; |
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have_eta_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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|
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// We need NkBT a lot, so just set it here: This is the RAW number |
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// of particles, so no subtraction or addition of constraints or |
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// orientational degrees of freedom: |
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|
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NkBT = (double)Nparticles * kB * targetTemp; |
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|
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// fkBT is used because the thermostat operates on more degrees of freedom |
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// than the barostat (when there are particles with orientational degrees |
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// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
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|
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fkBT = (double)info->ndf * kB * targetTemp; |
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|
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return 1; |
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} |
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|
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template<typename T> double NPTi<T>::getConservedQuantity(void){ |
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|
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double conservedQuantity; |
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double Three_NkBT; |
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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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double tb2; |
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double eta2; |
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|
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Energy = tStats->getTotalE(); |
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|
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thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
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(2.0 * eConvert); |
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|
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thermostat_potential = fkBT* integralOfChidt / eConvert; |
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|
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|
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barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / |
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(2.0 * eConvert); |
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|
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barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
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eConvert; |
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|
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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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cout.width(8); |
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cout.precision(8); |
| 431 |
|
| 432 |
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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|
| 436 |
return conservedQuantity; |
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} |
