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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 "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 non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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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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NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
27 |
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Integrator( theInfo, the_ff ) |
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template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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T( theInfo, the_ff ) |
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{ |
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int i, j; |
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chi = 0.0; |
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integralOfChidt = 0.0; |
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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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for (j = 0; j < 3; j++) |
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eta[i][j] = 0.0; |
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|
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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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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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< |
void NPTf::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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template<typename T> NPTf<T>::~NPTf() { |
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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 NPTf<T>::moveA() { |
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|
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// new version of NPTf |
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int i, j, k; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double ri[3], vi[3], sc[3]; |
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double instaTemp, instaVol; |
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double tt2, tb2, eta2ij; |
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double angle; |
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double Tb[3], ji[3]; |
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|
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double 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; |
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double sc[3]; |
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double eta2ij; |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
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double bigScale, smallScale, offDiagMax; |
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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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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor(press); |
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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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tStats->getCOM(COM); |
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|
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//calculate scale factor of veloity |
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for (i = 0; i < 3; i++ ) { |
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for (j = 0; j < 3; j++ ) { |
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vScale[i][j] = eta[i][j]; |
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|
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if (i == j) { |
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|
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eta[i][j] += dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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|
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vScale[i][j] = eta[i][j] + chi; |
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|
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} else { |
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|
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eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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|
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vScale[i][j] = eta[i][j]; |
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|
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} |
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vScale[i][j] += chi; |
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} |
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} |
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} |
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|
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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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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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|
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// velocity half step |
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|
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vi[0] = vel[atomIndex]; |
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vi[1] = vel[atomIndex+1]; |
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vi[2] = vel[atomIndex+2]; |
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|
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info->matVecMul3( vScale, vi, sc ); |
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|
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vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
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vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
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vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
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|
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vel[atomIndex] = vi[0] |
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vel[atomIndex+1] = vi[1]; |
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vel[atomIndex+2] = vi[2]; |
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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|
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// position whole step |
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mass = atoms[i]->getMass(); |
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|
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info->matVecMul3( vScale, vel, sc ); |
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|
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ri[0] = pos[atomIndex]; |
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ri[1] = pos[atomIndex+1]; |
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ri[2] = pos[atomIndex+2]; |
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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 - sc[j]); |
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} |
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|
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info->wrapVector(ri); |
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|
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info->matVecMul3( eta, ri, sc ); |
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|
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pos[atomIndex] += dt * (vel[atomIndex] + sc[0]); |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]); |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]); |
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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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|
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// get and convert the torque to body frame |
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|
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Tb[0] = dAtom->getTx(); |
122 |
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Tb[1] = dAtom->getTy(); |
123 |
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Tb[2] = dAtom->getTz(); |
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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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ji[0] = dAtom->getJx(); |
131 |
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ji[1] = dAtom->getJy(); |
132 |
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ji[2] = dAtom->getJz(); |
130 |
> |
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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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
136 |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
137 |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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|
139 |
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
141 |
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|
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// rotate about the x-axis |
143 |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
144 |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
147 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
148 |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
149 |
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|
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// rotate about the z-axis |
151 |
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angle = dt * ji[2] / dAtom->getIzz(); |
152 |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
153 |
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|
154 |
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// rotate about the y-axis |
155 |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
154 |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
155 |
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|
156 |
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// rotate about the x-axis |
157 |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
158 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
159 |
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|
160 |
< |
dAtom->setJx( ji[0] ); |
161 |
< |
dAtom->setJy( ji[1] ); |
162 |
< |
dAtom->setJz( ji[2] ); |
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> |
this->rotationPropagation( dAtom, ji ); |
136 |
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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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> |
// advance chi half step |
142 |
> |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
143 |
> |
|
144 |
> |
// calculate the integral of chidt |
145 |
> |
integralOfChidt += dt2*chi; |
146 |
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|
147 |
> |
// advance eta half step |
148 |
> |
|
149 |
> |
for(i = 0; i < 3; i ++) |
150 |
> |
for(j = 0; j < 3; j++){ |
151 |
> |
if( i == j) |
152 |
> |
eta[i][j] += dt2 * instaVol * |
153 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
154 |
> |
else |
155 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
156 |
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} |
157 |
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|
158 |
+ |
//save the old positions |
159 |
+ |
for(i = 0; i < nAtoms; i++){ |
160 |
+ |
atoms[i]->getPos(pos); |
161 |
+ |
for(j = 0; j < 3; j++) |
162 |
+ |
oldPos[i*3 + j] = pos[j]; |
163 |
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} |
164 |
+ |
|
165 |
+ |
//the first estimation of r(t+dt) is equal to r(t) |
166 |
+ |
|
167 |
+ |
for(k = 0; k < 4; k ++){ |
168 |
|
|
169 |
< |
// Scale the box after all the positions have been moved: |
169 |
> |
for(i =0 ; i < nAtoms; i++){ |
170 |
|
|
171 |
< |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
172 |
< |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
171 |
> |
atoms[i]->getVel(vel); |
172 |
> |
atoms[i]->getPos(pos); |
173 |
|
|
174 |
+ |
for(j = 0; j < 3; j++) |
175 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
176 |
+ |
|
177 |
+ |
info->matVecMul3( eta, rj, sc ); |
178 |
+ |
|
179 |
+ |
for(j = 0; j < 3; j++) |
180 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
181 |
|
|
182 |
+ |
atoms[i]->setPos( pos ); |
183 |
+ |
|
184 |
+ |
} |
185 |
+ |
|
186 |
+ |
if (nConstrained) { |
187 |
+ |
constrainA(); |
188 |
+ |
} |
189 |
+ |
} |
190 |
+ |
|
191 |
+ |
|
192 |
+ |
// Scale the box after all the positions have been moved: |
193 |
+ |
|
194 |
+ |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
195 |
+ |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
196 |
+ |
|
197 |
+ |
bigScale = 1.0; |
198 |
+ |
smallScale = 1.0; |
199 |
+ |
offDiagMax = 0.0; |
200 |
+ |
|
201 |
|
for(i=0; i<3; i++){ |
202 |
|
for(j=0; j<3; j++){ |
203 |
< |
|
203 |
> |
|
204 |
|
// Calculate the matrix Product of the eta array (we only need |
205 |
|
// the ij element right now): |
206 |
< |
|
206 |
> |
|
207 |
|
eta2ij = 0.0; |
208 |
|
for(k=0; k<3; k++){ |
209 |
|
eta2ij += eta[i][k] * eta[k][j]; |
215 |
|
// Taylor expansion for the exponential truncated at second order: |
216 |
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
217 |
|
|
218 |
+ |
if (i != j) |
219 |
+ |
if (fabs(scaleMat[i][j]) > offDiagMax) |
220 |
+ |
offDiagMax = fabs(scaleMat[i][j]); |
221 |
|
} |
222 |
+ |
|
223 |
+ |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
224 |
+ |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
225 |
|
} |
192 |
– |
|
193 |
– |
info->getBoxM(hm); |
194 |
– |
info->matMul3(hm, scaleMat, hmnew); |
195 |
– |
info->setBoxM(hmnew); |
226 |
|
|
227 |
+ |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
228 |
+ |
sprintf( painCave.errMsg, |
229 |
+ |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
230 |
+ |
" Check your tauBarostat, as it is probably too small!\n\n" |
231 |
+ |
" scaleMat = [%lf\t%lf\t%lf]\n" |
232 |
+ |
" [%lf\t%lf\t%lf]\n" |
233 |
+ |
" [%lf\t%lf\t%lf]\n", |
234 |
+ |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
235 |
+ |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
236 |
+ |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
237 |
+ |
painCave.isFatal = 1; |
238 |
+ |
simError(); |
239 |
+ |
} else if (offDiagMax > 0.1) { |
240 |
+ |
sprintf( painCave.errMsg, |
241 |
+ |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
242 |
+ |
" Check your tauBarostat, as it is probably too small!\n\n" |
243 |
+ |
" scaleMat = [%lf\t%lf\t%lf]\n" |
244 |
+ |
" [%lf\t%lf\t%lf]\n" |
245 |
+ |
" [%lf\t%lf\t%lf]\n", |
246 |
+ |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
247 |
+ |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
248 |
+ |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
249 |
+ |
painCave.isFatal = 1; |
250 |
+ |
simError(); |
251 |
+ |
} else { |
252 |
+ |
info->getBoxM(hm); |
253 |
+ |
info->matMul3(hm, scaleMat, hmnew); |
254 |
+ |
info->setBoxM(hmnew); |
255 |
+ |
} |
256 |
+ |
|
257 |
|
} |
258 |
|
|
259 |
< |
void NPTf::moveB( void ){ |
260 |
< |
int i,j, k; |
261 |
< |
int atomIndex; |
259 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
260 |
> |
|
261 |
> |
//new version of NPTf |
262 |
> |
int i, j, k; |
263 |
|
DirectionalAtom* dAtom; |
264 |
< |
double Tb[3]; |
265 |
< |
double ji[3]; |
266 |
< |
double vi[3], sc[3]; |
267 |
< |
double instaTemp, instaVol; |
264 |
> |
double Tb[3], ji[3]; |
265 |
> |
double vel[3], myVel[3], frc[3]; |
266 |
> |
double mass; |
267 |
> |
|
268 |
> |
double instaTemp, instaPress, instaVol; |
269 |
|
double tt2, tb2; |
270 |
+ |
double sc[3]; |
271 |
|
double press[3][3], vScale[3][3]; |
272 |
+ |
double oldChi, prevChi; |
273 |
+ |
double oldEta[3][3], prevEta[3][3], diffEta; |
274 |
|
|
275 |
|
tt2 = tauThermostat * tauThermostat; |
276 |
|
tb2 = tauBarostat * tauBarostat; |
277 |
|
|
278 |
< |
instaTemp = tStats->getTemperature(); |
279 |
< |
tStats->getPressureTensor(press); |
280 |
< |
instaVol = tStats->getVolume(); |
216 |
< |
|
217 |
< |
// first evolve chi a half step |
278 |
> |
// Set things up for the iteration: |
279 |
> |
|
280 |
> |
oldChi = chi; |
281 |
|
|
282 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
283 |
< |
|
284 |
< |
for (i = 0; i < 3; i++ ) { |
222 |
< |
for (j = 0; j < 3; j++ ) { |
223 |
< |
if (i == j) { |
282 |
> |
for(i = 0; i < 3; i++) |
283 |
> |
for(j = 0; j < 3; j++) |
284 |
> |
oldEta[i][j] = eta[i][j]; |
285 |
|
|
286 |
< |
eta[i][j] += dt2 * instaVol * |
226 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
286 |
> |
for( i=0; i<nAtoms; i++ ){ |
287 |
|
|
288 |
< |
vScale[i][j] = eta[i][j] + chi; |
229 |
< |
|
230 |
< |
} else { |
231 |
< |
|
232 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
288 |
> |
atoms[i]->getVel( vel ); |
289 |
|
|
290 |
< |
vScale[i][j] = eta[i][j]; |
291 |
< |
|
292 |
< |
} |
290 |
> |
for (j=0; j < 3; j++) |
291 |
> |
oldVel[3*i + j] = vel[j]; |
292 |
> |
|
293 |
> |
if( atoms[i]->isDirectional() ){ |
294 |
> |
|
295 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
296 |
> |
|
297 |
> |
dAtom->getJ( ji ); |
298 |
> |
|
299 |
> |
for (j=0; j < 3; j++) |
300 |
> |
oldJi[3*i + j] = ji[j]; |
301 |
> |
|
302 |
|
} |
303 |
|
} |
304 |
|
|
305 |
< |
for( i=0; i<nAtoms; i++ ){ |
241 |
< |
atomIndex = i * 3; |
305 |
> |
// do the iteration: |
306 |
|
|
307 |
< |
// velocity half step |
307 |
> |
instaVol = tStats->getVolume(); |
308 |
> |
|
309 |
> |
for (k=0; k < 4; k++) { |
310 |
|
|
311 |
< |
vi[0] = vel[atomIndex]; |
312 |
< |
vi[1] = vel[atomIndex+1]; |
313 |
< |
vi[2] = vel[atomIndex+2]; |
311 |
> |
instaTemp = tStats->getTemperature(); |
312 |
> |
tStats->getPressureTensor(press); |
313 |
> |
|
314 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
315 |
> |
|
316 |
> |
prevChi = chi; |
317 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
318 |
|
|
319 |
< |
info->matVecMul3( vScale, vi, sc ); |
320 |
< |
|
321 |
< |
vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
252 |
< |
vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
253 |
< |
vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
319 |
> |
for(i = 0; i < 3; i++) |
320 |
> |
for(j = 0; j < 3; j++) |
321 |
> |
prevEta[i][j] = eta[i][j]; |
322 |
|
|
323 |
< |
vel[atomIndex] = vi[0] |
324 |
< |
vel[atomIndex+1] = vi[1]; |
325 |
< |
vel[atomIndex+2] = vi[2]; |
323 |
> |
//advance eta half step and calculate scale factor for velocity |
324 |
> |
|
325 |
> |
for(i = 0; i < 3; i ++) |
326 |
> |
for(j = 0; j < 3; j++){ |
327 |
> |
if( i == j) { |
328 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
329 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
330 |
> |
vScale[i][j] = eta[i][j] + chi; |
331 |
> |
} else { |
332 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
333 |
> |
vScale[i][j] = eta[i][j]; |
334 |
> |
} |
335 |
> |
} |
336 |
|
|
337 |
< |
if( atoms[i]->isDirectional() ){ |
337 |
> |
for( i=0; i<nAtoms; i++ ){ |
338 |
> |
|
339 |
> |
atoms[i]->getFrc( frc ); |
340 |
> |
atoms[i]->getVel(vel); |
341 |
|
|
342 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
342 |
> |
mass = atoms[i]->getMass(); |
343 |
> |
|
344 |
> |
for (j = 0; j < 3; j++) |
345 |
> |
myVel[j] = oldVel[3*i + j]; |
346 |
|
|
347 |
< |
// get and convert the torque to body frame |
347 |
> |
info->matVecMul3( vScale, myVel, sc ); |
348 |
|
|
349 |
< |
Tb[0] = dAtom->getTx(); |
350 |
< |
Tb[1] = dAtom->getTy(); |
351 |
< |
Tb[2] = dAtom->getTz(); |
349 |
> |
// velocity half step |
350 |
> |
for (j=0; j < 3; j++) { |
351 |
> |
// velocity half step (use chi from previous step here): |
352 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
353 |
> |
} |
354 |
|
|
355 |
< |
dAtom->lab2Body( Tb ); |
355 |
> |
atoms[i]->setVel( vel ); |
356 |
|
|
357 |
< |
// get the angular momentum, and complete the angular momentum |
358 |
< |
// half step |
357 |
> |
if( atoms[i]->isDirectional() ){ |
358 |
> |
|
359 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
360 |
> |
|
361 |
> |
// get and convert the torque to body frame |
362 |
> |
|
363 |
> |
dAtom->getTrq( Tb ); |
364 |
> |
dAtom->lab2Body( Tb ); |
365 |
> |
|
366 |
> |
for (j=0; j < 3; j++) |
367 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
368 |
|
|
369 |
< |
ji[0] = dAtom->getJx(); |
370 |
< |
ji[1] = dAtom->getJy(); |
276 |
< |
ji[2] = dAtom->getJz(); |
277 |
< |
|
278 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
279 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
280 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
281 |
< |
|
282 |
< |
dAtom->setJx( ji[0] ); |
283 |
< |
dAtom->setJy( ji[1] ); |
284 |
< |
dAtom->setJz( ji[2] ); |
369 |
> |
dAtom->setJ( ji ); |
370 |
> |
} |
371 |
|
} |
372 |
+ |
|
373 |
+ |
if (nConstrained) { |
374 |
+ |
constrainB(); |
375 |
+ |
} |
376 |
+ |
|
377 |
+ |
diffEta = 0; |
378 |
+ |
for(i = 0; i < 3; i++) |
379 |
+ |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
380 |
+ |
|
381 |
+ |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
382 |
+ |
break; |
383 |
|
} |
384 |
+ |
|
385 |
+ |
//calculate integral of chidt |
386 |
+ |
integralOfChidt += dt2*chi; |
387 |
+ |
|
388 |
|
} |
389 |
|
|
390 |
< |
int NPTf::readyCheck() { |
390 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
391 |
> |
int i,j; |
392 |
> |
|
393 |
> |
chi = 0.0; |
394 |
> |
|
395 |
> |
for(i = 0; i < 3; i++) |
396 |
> |
for (j = 0; j < 3; j++) |
397 |
> |
eta[i][j] = 0.0; |
398 |
> |
|
399 |
> |
} |
400 |
> |
|
401 |
> |
template<typename T> int NPTf<T>::readyCheck() { |
402 |
> |
|
403 |
> |
//check parent's readyCheck() first |
404 |
> |
if (T::readyCheck() == -1) |
405 |
> |
return -1; |
406 |
|
|
407 |
|
// First check to see if we have a target temperature. |
408 |
|
// Not having one is fatal. |
449 |
|
return -1; |
450 |
|
} |
451 |
|
|
452 |
< |
// We need NkBT a lot, so just set it here: |
452 |
> |
|
453 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
454 |
> |
// of particles, so no subtraction or addition of constraints or |
455 |
> |
// orientational degrees of freedom: |
456 |
> |
|
457 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
458 |
> |
|
459 |
> |
// fkBT is used because the thermostat operates on more degrees of freedom |
460 |
> |
// than the barostat (when there are particles with orientational degrees |
461 |
> |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
462 |
> |
|
463 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
464 |
|
|
338 |
– |
NkBT = (double)info->ndf * kB * targetTemp; |
339 |
– |
|
465 |
|
return 1; |
466 |
|
} |
467 |
+ |
|
468 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
469 |
+ |
|
470 |
+ |
double conservedQuantity; |
471 |
+ |
double Energy; |
472 |
+ |
double thermostat_kinetic; |
473 |
+ |
double thermostat_potential; |
474 |
+ |
double barostat_kinetic; |
475 |
+ |
double barostat_potential; |
476 |
+ |
double trEta; |
477 |
+ |
double a[3][3], b[3][3]; |
478 |
+ |
|
479 |
+ |
Energy = tStats->getTotalE(); |
480 |
+ |
|
481 |
+ |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
482 |
+ |
(2.0 * eConvert); |
483 |
+ |
|
484 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
485 |
+ |
|
486 |
+ |
info->transposeMat3(eta, a); |
487 |
+ |
info->matMul3(a, eta, b); |
488 |
+ |
trEta = info->matTrace3(b); |
489 |
+ |
|
490 |
+ |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
491 |
+ |
(2.0 * eConvert); |
492 |
+ |
|
493 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
494 |
+ |
eConvert; |
495 |
+ |
|
496 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
497 |
+ |
barostat_kinetic + barostat_potential; |
498 |
+ |
|
499 |
+ |
cout.width(8); |
500 |
+ |
cout.precision(8); |
501 |
+ |
|
502 |
+ |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
503 |
+ |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
504 |
+ |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
505 |
+ |
|
506 |
+ |
return conservedQuantity; |
507 |
+ |
} |