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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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// Basic non-isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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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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template<typename T> NPTf<T>::~NPTf() { |
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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], ji[3]; |
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double A[3][3], I[3][3]; |
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double angle, mass; |
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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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info->matVecMul3( vScale, vel, sc ); |
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for (j=0; j < 3; j++) { |
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// velocity half step (use chi from previous step here): |
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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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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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dAtom->getA(A); |
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dAtom->getI(I); |
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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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// 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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// 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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this->rotationPropagation( dAtom, ji ); |
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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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// 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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// calculate the integral of chidt |
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integralOfChidt += dt2*chi; |
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//advance eta half step |
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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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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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} |
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if (nConstrained) { |
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constrainA(); |
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} |
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} |
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template<typename T> void NPTf<T>::moveB( void ){ |
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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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double vel[3], frc[3]; |
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double vel[3], myVel[3], frc[3]; |
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double mass; |
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double instaTemp, instaPress, instaVol; |
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double sc[3]; |
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double press[3][3], vScale[3][3]; |
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double oldChi, prevChi; |
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double oldEta[3][3], preEta[3][3], diffEta; |
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double oldEta[3][3], prevEta[3][3], diffEta; |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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// Set things up for the iteration: |
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oldChi = chi; |
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for(i = 0; i < 3; i++) |
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for(j = 0; j < 3; j++) |
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preEta[i][j] = eta[i][j]; |
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> |
prevEta[i][j] = eta[i][j]; |
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//advance eta half step and calculate scale factor for velocity |
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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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if( i == j) { |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
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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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} else { |
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eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
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vScale[i][j] = eta[i][j]; |
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} |
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< |
} |
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< |
|
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//advance velocity half step |
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} |
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> |
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getFrc( frc ); |
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atoms[i]->getVel(vel); |
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mass = atoms[i]->getMass(); |
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+ |
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+ |
for (j = 0; j < 3; j++) |
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myVel[j] = oldVel[3*i + j]; |
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|
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< |
info->matVecMul3( vScale, vel, sc ); |
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< |
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> |
info->matVecMul3( vScale, myVel, sc ); |
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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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// velocity half step (use chi from previous step here): |
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
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} |
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} |
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|
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+ |
if (nConstrained) { |
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+ |
constrainB(); |
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+ |
} |
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diffEta = 0; |
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for(i = 0; i < 3; i++) |
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< |
diffEta += pow(preEta[i][i] - eta[i][i], 2); |
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> |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
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if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
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break; |
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} |
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< |
//calculate integral of chida |
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> |
//calculate integral of chidt |
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integralOfChidt += dt2*chi; |
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} |
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return -1; |
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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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> |
|
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> |
// We need NkBT a lot, so just set it here: This is the RAW number |
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> |
// of particles, so no subtraction or addition of constraints or |
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> |
// orientational degrees of freedom: |
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> |
|
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NkBT = (double)Nparticles * kB * targetTemp; |
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+ |
|
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+ |
// fkBT is used because the thermostat operates on more degrees of freedom |
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+ |
// than the barostat (when there are particles with orientational degrees |
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+ |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
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+ |
|
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fkBT = (double)info->ndf * kB * targetTemp; |
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return 1; |
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template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 469 |
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|
| 470 |
|
double conservedQuantity; |
| 471 |
< |
double tb2; |
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< |
double trEta; |
| 473 |
< |
double U; |
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< |
double thermo; |
| 475 |
< |
double integral; |
| 476 |
< |
double baro; |
| 477 |
< |
double PV; |
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> |
double Energy; |
| 472 |
> |
double thermostat_kinetic; |
| 473 |
> |
double thermostat_potential; |
| 474 |
> |
double barostat_kinetic; |
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> |
double barostat_potential; |
| 476 |
> |
double trEta; |
| 477 |
> |
double a[3][3], b[3][3]; |
| 478 |
|
|
| 479 |
< |
U = tStats->getTotalE(); |
| 485 |
< |
thermo = (fkBT * tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
| 479 |
> |
Energy = tStats->getTotalE(); |
| 480 |
|
|
| 481 |
< |
tb2 = tauBarostat * tauBarostat; |
| 482 |
< |
trEta = info->matTrace3(eta); |
| 489 |
< |
baro = ((double)info->ndfTrans * kB * targetTemp * tb2 * trEta * trEta / 2.0) / eConvert; |
| 481 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 482 |
> |
(2.0 * eConvert); |
| 483 |
|
|
| 484 |
< |
integral = ((double)(info->ndf + 1) * kB * targetTemp * integralOfChidt) /eConvert; |
| 484 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 485 |
|
|
| 486 |
< |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
| 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); |
| 498 |
– |
|
| 499 |
– |
cout << info->getTime() << "\t" |
| 500 |
– |
<< chi << "\t" |
| 501 |
– |
<< trEta << "\t" |
| 502 |
– |
<< U << "\t" |
| 503 |
– |
<< thermo << "\t" |
| 504 |
– |
<< baro << "\t" |
| 505 |
– |
<< integral << "\t" |
| 506 |
– |
<< PV << "\t" |
| 507 |
– |
<< U+thermo+integral+PV+baro << endl; |
| 501 |
|
|
| 502 |
< |
conservedQuantity = U+thermo+integral+PV+baro; |
| 503 |
< |
return conservedQuantity; |
| 504 |
< |
|
| 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 |
|
} |
