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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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integralOfChidt = integralOfChidtValue->getData(); |
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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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oldPos = new double[3*integrableObjects.size()]; |
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oldVel = new double[3*integrableObjects.size()]; |
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oldJi = new double[3*integrableObjects.size()]; |
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#ifdef IS_MPI |
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Nparticles = mpiSim->getTotAtoms(); |
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#else |
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//new version of NPT |
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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 mass; |
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double vel[3], pos[3], frc[3]; |
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tStats->getCOM(COM); |
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//evolve velocity half step |
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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calcVelScale(); |
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for( i=0; i<integrableObjects.size(); i++ ){ |
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mass = atoms[i]->getMass(); |
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integrableObjects[i]->getVel( vel ); |
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integrableObjects[i]->getFrc( frc ); |
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mass = integrableObjects[i]->getMass(); |
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getVelScaleA( sc, vel ); |
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for (j=0; j < 3; j++) { |
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} |
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atoms[i]->setVel( vel ); |
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integrableObjects[i]->setVel( vel ); |
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if( atoms[i]->isDirectional() ){ |
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if( integrableObjects[i]->isDirectional() ){ |
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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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integrableObjects[i]->getTrq( Tb ); |
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integrableObjects[i]->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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dAtom->getJ( ji ); |
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integrableObjects[i]->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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this->rotationPropagation( dAtom, ji ); |
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this->rotationPropagation( integrableObjects[i], ji ); |
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dAtom->setJ( ji ); |
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integrableObjects[i]->setJ( ji ); |
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} |
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} |
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integralOfChidt += dt2*chi; |
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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(i = 0; i < integrableObjects.size(); i++){ |
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integrableObjects[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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for(k = 0; k < 5; k ++){ |
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for(i =0 ; i < nAtoms; i++){ |
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for(i =0 ; i < integrableObjects.size(); i++){ |
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atoms[i]->getVel(vel); |
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atoms[i]->getPos(pos); |
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integrableObjects[i]->getVel(vel); |
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integrableObjects[i]->getPos(pos); |
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this->getPosScale( pos, COM, i, sc ); |
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for(j = 0; j < 3; j++) |
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pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
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atoms[i]->setPos( pos ); |
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integrableObjects[i]->setPos( pos ); |
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} |
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if (nConstrained){ |
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//new version of NPT |
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int i, j, k; |
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DirectionalAtom* dAtom; |
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double Tb[3], ji[3], sc[3]; |
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double vel[3], frc[3]; |
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double mass; |
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// Set things up for the iteration: |
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for( i=0; i<nAtoms; i++ ){ |
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for( i=0; i<integrableObjects.size(); i++ ){ |
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atoms[i]->getVel( vel ); |
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integrableObjects[i]->getVel( vel ); |
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
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if( atoms[i]->isDirectional() ){ |
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if( integrableObjects[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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integrableObjects[i]->getJ( ji ); |
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dAtom->getJ( ji ); |
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for (j=0; j < 3; j++) |
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oldJi[3*i + j] = ji[j]; |
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this->evolveChiB(); |
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this->evolveEtaB(); |
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this->calcVelScale(); |
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for( i=0; i<nAtoms; i++ ){ |
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for( i=0; i<integrableObjects.size(); i++ ){ |
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atoms[i]->getFrc( frc ); |
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atoms[i]->getVel(vel); |
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integrableObjects[i]->getFrc( frc ); |
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integrableObjects[i]->getVel(vel); |
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mass = atoms[i]->getMass(); |
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mass = integrableObjects[i]->getMass(); |
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getVelScaleB( sc, i ); |
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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 - sc[j]); |
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atoms[i]->setVel( vel ); |
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integrableObjects[i]->setVel( vel ); |
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if( atoms[i]->isDirectional() ){ |
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if( integrableObjects[i]->isDirectional() ){ |
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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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integrableObjects[i]->getTrq( Tb ); |
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integrableObjects[i]->lab2Body( Tb ); |
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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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dAtom->setJ( ji ); |
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integrableObjects[i]->setJ( ji ); |
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} |
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} |
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