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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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#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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// 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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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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eta[i][j] = 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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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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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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template<typename T> void NPTf<T>::moveA() { |
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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], 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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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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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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if (i == j) { |
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vScale[i][j] += chi; |
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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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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
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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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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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atoms[i]->setVel( vel ); |
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if( atoms[i]->isDirectional() ){ |
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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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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
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// get the angular momentum, and propagate a half step |
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dAtom->getJ( ji ); |
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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this->rotationPropagation( dAtom, ji ); |
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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 |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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// calculate the integral of chidt |
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integralOfChidt += dt2*chi; |
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// advance eta half step |
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for(i = 0; i < 3; i ++) |
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for(j = 0; j < 3; j++){ |
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if( i == j) |
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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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else |
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eta[i][j] += dt2 * instaVol * press[i][j] / (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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//the first estimation of r(t+dt) is equal to r(t) |
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for(k = 0; k < 4; k ++){ |
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for(i =0 ; i < nAtoms; i++){ |
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atoms[i]->getVel(vel); |
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atoms[i]->getPos(pos); |
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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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info->matVecMul3( eta, rj, 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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} |
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if (nConstrained) { |
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constrainA(); |
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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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// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
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// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
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bigScale = 1.0; |
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smallScale = 1.0; |
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offDiagMax = 0.0; |
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for(i=0; i<3; i++){ |
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for(j=0; j<3; j++){ |
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|
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// Calculate the matrix Product of the eta array (we only need |
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// the ij element right now): |
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|
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eta2ij = 0.0; |
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for(k=0; k<3; k++){ |
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eta2ij += eta[i][k] * eta[k][j]; |
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} |
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scaleMat[i][j] = 0.0; |
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// identity matrix (see above): |
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if (i == j) scaleMat[i][j] = 1.0; |
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// Taylor expansion for the exponential truncated at second order: |
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scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
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if (i != j) |
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if (fabs(scaleMat[i][j]) > offDiagMax) |
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offDiagMax = fabs(scaleMat[i][j]); |
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} |
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if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
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if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
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} |
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|
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if ((bigScale > 1.1) || (smallScale < 0.9)) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else if (offDiagMax > 0.1) { |
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sprintf( painCave.errMsg, |
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"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
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" Check your tauBarostat, as it is probably too small!\n\n" |
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" scaleMat = [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n" |
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" [%lf\t%lf\t%lf]\n", |
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scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
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scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
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scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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info->getBoxM(hm); |
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info->matMul3(hm, scaleMat, hmnew); |
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info->setBoxM(hmnew); |
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} |
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gezelter |
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gezelter |
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} |
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tim |
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template<typename T> void NPTf<T>::moveB( void ){ |
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gezelter |
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|
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gezelter |
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//new version of NPTf |
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tim |
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int i, j, k; |
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gezelter |
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DirectionalAtom* dAtom; |
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gezelter |
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double Tb[3], ji[3]; |
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gezelter |
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double vel[3], myVel[3], frc[3]; |
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gezelter |
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double mass; |
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double instaTemp, instaPress, instaVol; |
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gezelter |
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double tt2, tb2; |
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gezelter |
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double sc[3]; |
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gezelter |
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double press[3][3], vScale[3][3]; |
272 |
tim |
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double oldChi, prevChi; |
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gezelter |
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double oldEta[3][3], prevEta[3][3], diffEta; |
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gezelter |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
277 |
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tim |
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// Set things up for the iteration: |
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oldChi = chi; |
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gezelter |
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|
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tim |
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for(i = 0; i < 3; i++) |
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for(j = 0; j < 3; j++) |
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oldEta[i][j] = eta[i][j]; |
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gezelter |
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|
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tim |
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for( i=0; i<nAtoms; i++ ){ |
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gezelter |
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|
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tim |
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atoms[i]->getVel( vel ); |
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gezelter |
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|
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tim |
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
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293 |
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if( atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)atoms[i]; |
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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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gezelter |
588 |
} |
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} |
304 |
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305 |
tim |
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// do the iteration: |
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gezelter |
578 |
|
307 |
tim |
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instaVol = tStats->getVolume(); |
308 |
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for (k=0; k < 4; k++) { |
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gezelter |
600 |
|
311 |
tim |
767 |
instaTemp = tStats->getTemperature(); |
312 |
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tStats->getPressureTensor(press); |
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gezelter |
578 |
|
314 |
tim |
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// evolve chi another half step using the temperature at t + dt/2 |
315 |
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prevChi = chi; |
317 |
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chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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gezelter |
578 |
|
319 |
tim |
767 |
for(i = 0; i < 3; i++) |
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for(j = 0; j < 3; j++) |
321 |
gezelter |
772 |
prevEta[i][j] = eta[i][j]; |
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gezelter |
600 |
|
323 |
tim |
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//advance eta half step and calculate scale factor for velocity |
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gezelter |
772 |
|
325 |
tim |
767 |
for(i = 0; i < 3; i ++) |
326 |
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for(j = 0; j < 3; j++){ |
327 |
gezelter |
772 |
if( i == j) { |
328 |
tim |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
329 |
gezelter |
772 |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
330 |
tim |
767 |
vScale[i][j] = eta[i][j] + chi; |
331 |
gezelter |
772 |
} else { |
332 |
tim |
767 |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
333 |
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vScale[i][j] = eta[i][j]; |
334 |
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} |
335 |
gezelter |
772 |
} |
336 |
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337 |
tim |
767 |
for( i=0; i<nAtoms; i++ ){ |
338 |
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339 |
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atoms[i]->getFrc( frc ); |
340 |
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atoms[i]->getVel(vel); |
341 |
gezelter |
576 |
|
342 |
tim |
767 |
mass = atoms[i]->getMass(); |
343 |
gezelter |
772 |
|
344 |
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for (j = 0; j < 3; j++) |
345 |
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myVel[j] = oldVel[3*i + j]; |
346 |
gezelter |
576 |
|
347 |
gezelter |
772 |
info->matVecMul3( vScale, myVel, sc ); |
348 |
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349 |
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// velocity half step |
350 |
tim |
767 |
for (j=0; j < 3; j++) { |
351 |
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// velocity half step (use chi from previous step here): |
352 |
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
353 |
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} |
354 |
gezelter |
576 |
|
355 |
tim |
767 |
atoms[i]->setVel( vel ); |
356 |
gezelter |
576 |
|
357 |
tim |
767 |
if( atoms[i]->isDirectional() ){ |
358 |
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359 |
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dAtom = (DirectionalAtom *)atoms[i]; |
360 |
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361 |
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// 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 |
gezelter |
576 |
|
369 |
tim |
767 |
dAtom->setJ( ji ); |
370 |
|
|
} |
371 |
|
|
} |
372 |
gezelter |
600 |
|
373 |
gezelter |
772 |
if (nConstrained) { |
374 |
|
|
constrainB(); |
375 |
|
|
} |
376 |
tim |
767 |
|
377 |
|
|
diffEta = 0; |
378 |
|
|
for(i = 0; i < 3; i++) |
379 |
gezelter |
772 |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
380 |
tim |
767 |
|
381 |
|
|
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
382 |
|
|
break; |
383 |
gezelter |
576 |
} |
384 |
tim |
767 |
|
385 |
gezelter |
772 |
//calculate integral of chidt |
386 |
tim |
767 |
integralOfChidt += dt2*chi; |
387 |
|
|
|
388 |
gezelter |
576 |
} |
389 |
|
|
|
390 |
mmeineke |
746 |
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 |
tim |
645 |
template<typename T> int NPTf<T>::readyCheck() { |
402 |
tim |
658 |
|
403 |
|
|
//check parent's readyCheck() first |
404 |
|
|
if (T::readyCheck() == -1) |
405 |
|
|
return -1; |
406 |
gezelter |
576 |
|
407 |
|
|
// First check to see if we have a target temperature. |
408 |
|
|
// Not having one is fatal. |
409 |
|
|
|
410 |
|
|
if (!have_target_temp) { |
411 |
|
|
sprintf( painCave.errMsg, |
412 |
gezelter |
580 |
"NPTf error: You can't use the NPTf integrator\n" |
413 |
gezelter |
576 |
" without a targetTemp!\n" |
414 |
|
|
); |
415 |
|
|
painCave.isFatal = 1; |
416 |
|
|
simError(); |
417 |
|
|
return -1; |
418 |
|
|
} |
419 |
|
|
|
420 |
|
|
if (!have_target_pressure) { |
421 |
|
|
sprintf( painCave.errMsg, |
422 |
gezelter |
580 |
"NPTf error: You can't use the NPTf integrator\n" |
423 |
gezelter |
576 |
" without a targetPressure!\n" |
424 |
|
|
); |
425 |
|
|
painCave.isFatal = 1; |
426 |
|
|
simError(); |
427 |
|
|
return -1; |
428 |
|
|
} |
429 |
|
|
|
430 |
|
|
// We must set tauThermostat. |
431 |
|
|
|
432 |
|
|
if (!have_tau_thermostat) { |
433 |
|
|
sprintf( painCave.errMsg, |
434 |
gezelter |
580 |
"NPTf error: If you use the NPTf\n" |
435 |
gezelter |
576 |
" integrator, you must set tauThermostat.\n"); |
436 |
|
|
painCave.isFatal = 1; |
437 |
|
|
simError(); |
438 |
|
|
return -1; |
439 |
|
|
} |
440 |
|
|
|
441 |
|
|
// We must set tauBarostat. |
442 |
|
|
|
443 |
|
|
if (!have_tau_barostat) { |
444 |
|
|
sprintf( painCave.errMsg, |
445 |
gezelter |
580 |
"NPTf error: If you use the NPTf\n" |
446 |
gezelter |
576 |
" integrator, you must set tauBarostat.\n"); |
447 |
|
|
painCave.isFatal = 1; |
448 |
|
|
simError(); |
449 |
|
|
return -1; |
450 |
|
|
} |
451 |
|
|
|
452 |
gezelter |
772 |
|
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 |
tim |
767 |
NkBT = (double)Nparticles * kB * targetTemp; |
458 |
gezelter |
772 |
|
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 |
tim |
767 |
fkBT = (double)info->ndf * kB * targetTemp; |
464 |
gezelter |
576 |
|
465 |
|
|
return 1; |
466 |
|
|
} |
467 |
tim |
763 |
|
468 |
|
|
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
469 |
|
|
|
470 |
|
|
double conservedQuantity; |
471 |
gezelter |
772 |
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 |
tim |
763 |
|
479 |
gezelter |
772 |
Energy = tStats->getTotalE(); |
480 |
tim |
763 |
|
481 |
gezelter |
772 |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
482 |
|
|
(2.0 * eConvert); |
483 |
tim |
763 |
|
484 |
gezelter |
772 |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
485 |
tim |
763 |
|
486 |
gezelter |
772 |
info->transposeMat3(eta, a); |
487 |
|
|
info->matMul3(a, eta, b); |
488 |
|
|
trEta = info->matTrace3(b); |
489 |
tim |
767 |
|
490 |
gezelter |
772 |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
491 |
|
|
(2.0 * eConvert); |
492 |
|
|
|
493 |
|
|
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
494 |
|
|
eConvert; |
495 |
tim |
767 |
|
496 |
gezelter |
772 |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
497 |
|
|
barostat_kinetic + barostat_potential; |
498 |
|
|
|
499 |
tim |
767 |
cout.width(8); |
500 |
|
|
cout.precision(8); |
501 |
|
|
|
502 |
gezelter |
772 |
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 |
tim |
763 |
} |