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#include <cmath> |
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#include "Atom.hpp" |
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#include "Molecule.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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|
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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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// The NPTxym variant scales the molecular center-of-mass coordinates |
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// instead of the atomic coordinates |
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|
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template<typename T> NPTxym<T>::NPTxym ( 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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etaX = 0.0; |
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etaY = 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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} |
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|
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template<typename T> void NPTxym<T>::moveA() { |
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|
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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, instaPressZ, instaVol; |
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double tt2, tb2; |
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double scaleFactor, scaleFactorZ, scaleFactorX, scaleFactorY, bigFactor; |
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double hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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double scF3; |
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|
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|
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int nInMol; |
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double rc[3]; |
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|
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nMols = info->n_mol; |
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myMolecules = info->molecules; |
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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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instaPressX = tStats->getPressureX(); |
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instaPressY = tstats->getPressureY(); |
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instaVol = tStats->getVolume(); |
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|
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// first evolve chi a half step |
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|
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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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etaX += dt2 * ( instaVol * (instaPressX - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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etaY += dt2 * ( instaVol * (instaPressY - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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|
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for( i = 0; i < nMols; i++) { |
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|
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myMolecules[i].getCOM(rc); |
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|
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nInMol = myMolecules[i].getNAtoms(); |
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myAtoms = myMolecules[i].getMyAtoms(); |
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|
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// find the minimum image coordinates of the molecular centers of mass: |
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|
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info->wrapVector(rc); |
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|
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for (j = 0; j < nInMol; j++) { |
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|
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if(myAtoms[j] != NULL) { |
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|
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myAtoms[j]->getVel( vel ); |
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myAtoms[j]->getPos( pos ); |
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myAtoms[j]->getFrc( frc ); |
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|
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mass = myAtoms[j]->getMass(); |
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|
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for (k=0; k < 3; k++) |
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vel[k] += dt2 * ((frc[k] / mass ) * eConvert - vel[k]*(chi+eta)); |
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|
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myAtoms[j]->setVel( vel ); |
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|
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for (k = 0; k < 3; k++) |
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pos[k] += dt * (vel[k] + eta*rc[k]); |
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|
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myAtoms[j]->setPos( pos ); |
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|
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if( myAtoms[j]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)myAtoms[j]; |
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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 (k=0; k < 3; k++) |
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ji[k] += dt2 * (Tb[k] * eConvert - ji[k]*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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} |
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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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scaleFactorX = exp(dt*etaX); |
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scaleFactorY = exp(dt*etaY); |
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scaleFactor = exp(dt*eta); |
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|
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bigFactor = abs( 1.0 - scaleFactorX ); |
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if( abs(1.0 - scaleFactorY) > bigFactor ) |
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bigFactor = abs(1.0 - scaleFactorY); |
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if( abs(1.0 - scaleFactor) > bigFactor ) |
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bigFactor = abs(1.0 - scaleFactor); |
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|
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if (bigFactor > 0.1) { |
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sprintf( painCave.errMsg, |
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"NPTxym 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" |
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" etaX = %lf, scaleFactorX = %lf\n", |
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" etaY = %lf, scaleFactorY = %lf\n", |
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eta, scaleFactor, |
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etaX, scaleFactorX, |
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etaY, scaleFactorY |
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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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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) |
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scaleBox[i][j] = 0.0; |
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|
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scF3 = scaleFactor * scaleFactor * scaleFactor; |
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scaleFactorZ = scF3 / (scaleFactorX * scaleFactorY); |
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|
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scaleBox[0][0] = scaleFactorX; |
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scaleBox[1][1] = scaleFactorY; |
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scaleBox[2][2] = scaleFactorZ; |
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|
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info->getBoxM( hm ); |
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info->matMul3( hm, scaleBox, hmnew ); |
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|
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info->setBoxM( hmnew ); |
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} |
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} |
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|
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template<typename T> void NPTxym<T>::moveB( void ){ |
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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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|
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double instaTemp, instaPress, instaPressX, instaPressY, instaVol; |
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double tt2, tb2; |
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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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instaPressX = tStats->getPressureX(); |
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instaPressY = tstats->getPressureY(); |
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instaVol = tStats->getVolume(); |
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|
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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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etaX += dt2 * ( instaVol * (instaPressX - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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etaY += dt2 * ( instaVol * (instaPressY - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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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]->getFrc( frc ); |
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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] += dt2 * ((frc[j] / mass ) * eConvert - vel[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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// 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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dAtom->setJ( ji ); |
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} |
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} |
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} |
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|
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template<typename T> void NPTxym<T>::resetIntegrator() { |
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chi = 0.0; |
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eta = 0.0; |
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etaX = 0.0; |
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etaY = 0.0; |
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} |
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|
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template<typename T> int NPTxym<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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"NPTxym error: You can't use the NPTxym 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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"NPTxym error: You can't use the NPTxym 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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"NPTxym error: If you use the NPTxym\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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"NPTxym error: If you use the NPTxym\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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} |
