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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 isotropic thermostating and barostating via the Melchionna |
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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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// |
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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): |
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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; |
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int i, j; |
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chi = 0.0; |
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for(i = 0; i < 9; i++) eta[i] = 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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|
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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 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, instaVol; |
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double tt2, tb2; |
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double angle; |
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double press[9]; |
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const double p_convert = 1.63882576e8; |
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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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|
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instaTemp = tStats->getTemperature(); |
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tStats->getPressureTensor(press); |
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|
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for (i=0; i < 9; i++) press[i] *= p_convert; |
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|
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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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vScale[i][j] += chi; |
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} |
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} |
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} |
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|
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eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
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eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
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eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
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eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
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eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
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eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
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eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
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eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
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eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
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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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vx = vel[atomIndex]; |
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vy = vel[atomIndex+1]; |
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vz = vel[atomIndex+2]; |
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|
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scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
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scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
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scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
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|
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vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
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vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
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vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
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|
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vel[atomIndex] = vx; |
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vel[atomIndex+1] = vy; |
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vel[atomIndex+2] = vz; |
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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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< |
rj[0] = pos[atomIndex]; |
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< |
rj[1] = pos[atomIndex+1]; |
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< |
rj[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(rj); |
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< |
|
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< |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
| 103 |
< |
scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
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< |
scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
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< |
|
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< |
pos[atomIndex] += dt * (vel[atomIndex] + scx); |
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< |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
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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(); |
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< |
Tb[1] = dAtom->getTy(); |
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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(); |
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ji[1] = dAtom->getJy(); |
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< |
ji[2] = dAtom->getJz(); |
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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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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*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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> |
|
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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] / dAtom->getIxx(); |
| 143 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 144 |
< |
|
| 142 |
> |
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 |
| 146 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 147 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 146 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 147 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 148 |
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|
| 149 |
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// rotate about the z-axis |
| 150 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
| 151 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
| 150 |
> |
angle = dt * ji[2] / I[2][2]; |
| 151 |
> |
this->rotate( 0, 1, angle, ji, A); |
| 152 |
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|
| 153 |
|
// rotate about the y-axis |
| 154 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 155 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
| 154 |
> |
angle = dt2 * ji[1] / I[1][1]; |
| 155 |
> |
this->rotate( 2, 0, angle, ji, A ); |
| 156 |
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|
| 157 |
|
// rotate about the x-axis |
| 158 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 159 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
| 158 |
> |
angle = dt2 * ji[0] / I[0][0]; |
| 159 |
> |
this->rotate( 1, 2, angle, ji, A ); |
| 160 |
|
|
| 161 |
< |
dAtom->setJx( ji[0] ); |
| 162 |
< |
dAtom->setJy( ji[1] ); |
| 163 |
< |
dAtom->setJz( ji[2] ); |
| 161 |
> |
dAtom->setJ( ji ); |
| 162 |
> |
dAtom->setA( A ); |
| 163 |
> |
} |
| 164 |
> |
} |
| 165 |
> |
|
| 166 |
> |
// advance chi half step |
| 167 |
> |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 168 |
> |
|
| 169 |
> |
// calculate the integral of chidt |
| 170 |
> |
integralOfChidt += dt2*chi; |
| 171 |
> |
|
| 172 |
> |
// advance eta half step |
| 173 |
> |
|
| 174 |
> |
for(i = 0; i < 3; i ++) |
| 175 |
> |
for(j = 0; j < 3; j++){ |
| 176 |
> |
if( i == j) |
| 177 |
> |
eta[i][j] += dt2 * instaVol * |
| 178 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 179 |
> |
else |
| 180 |
> |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 181 |
|
} |
| 182 |
|
|
| 183 |
+ |
//save the old positions |
| 184 |
+ |
for(i = 0; i < nAtoms; i++){ |
| 185 |
+ |
atoms[i]->getPos(pos); |
| 186 |
+ |
for(j = 0; j < 3; j++) |
| 187 |
+ |
oldPos[i*3 + j] = pos[j]; |
| 188 |
|
} |
| 161 |
– |
|
| 162 |
– |
// Scale the box after all the positions have been moved: |
| 189 |
|
|
| 190 |
+ |
//the first estimation of r(t+dt) is equal to r(t) |
| 191 |
+ |
|
| 192 |
+ |
for(k = 0; k < 4; k ++){ |
| 193 |
|
|
| 194 |
+ |
for(i =0 ; i < nAtoms; i++){ |
| 195 |
|
|
| 196 |
< |
// Use a taylor expansion for eta products |
| 197 |
< |
|
| 168 |
< |
info->getBoxM(hm); |
| 169 |
< |
|
| 196 |
> |
atoms[i]->getVel(vel); |
| 197 |
> |
atoms[i]->getPos(pos); |
| 198 |
|
|
| 199 |
+ |
for(j = 0; j < 3; j++) |
| 200 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
| 201 |
+ |
|
| 202 |
+ |
info->matVecMul3( eta, rj, sc ); |
| 203 |
+ |
|
| 204 |
+ |
for(j = 0; j < 3; j++) |
| 205 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
| 206 |
|
|
| 207 |
+ |
atoms[i]->setPos( pos ); |
| 208 |
|
|
| 209 |
+ |
} |
| 210 |
|
|
| 211 |
+ |
if (nConstrained) { |
| 212 |
+ |
constrainA(); |
| 213 |
+ |
} |
| 214 |
+ |
} |
| 215 |
|
|
| 216 |
< |
info->scaleBox(exp(dt*eta)); |
| 216 |
> |
|
| 217 |
> |
// Scale the box after all the positions have been moved: |
| 218 |
> |
|
| 219 |
> |
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
| 220 |
> |
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
| 221 |
> |
|
| 222 |
> |
bigScale = 1.0; |
| 223 |
> |
smallScale = 1.0; |
| 224 |
> |
offDiagMax = 0.0; |
| 225 |
> |
|
| 226 |
> |
for(i=0; i<3; i++){ |
| 227 |
> |
for(j=0; j<3; j++){ |
| 228 |
> |
|
| 229 |
> |
// Calculate the matrix Product of the eta array (we only need |
| 230 |
> |
// the ij element right now): |
| 231 |
> |
|
| 232 |
> |
eta2ij = 0.0; |
| 233 |
> |
for(k=0; k<3; k++){ |
| 234 |
> |
eta2ij += eta[i][k] * eta[k][j]; |
| 235 |
> |
} |
| 236 |
> |
|
| 237 |
> |
scaleMat[i][j] = 0.0; |
| 238 |
> |
// identity matrix (see above): |
| 239 |
> |
if (i == j) scaleMat[i][j] = 1.0; |
| 240 |
> |
// Taylor expansion for the exponential truncated at second order: |
| 241 |
> |
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
| 242 |
|
|
| 243 |
+ |
if (i != j) |
| 244 |
+ |
if (fabs(scaleMat[i][j]) > offDiagMax) |
| 245 |
+ |
offDiagMax = fabs(scaleMat[i][j]); |
| 246 |
+ |
} |
| 247 |
|
|
| 248 |
+ |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
| 249 |
+ |
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
| 250 |
+ |
} |
| 251 |
+ |
|
| 252 |
+ |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
| 253 |
+ |
sprintf( painCave.errMsg, |
| 254 |
+ |
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
| 255 |
+ |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 256 |
+ |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 257 |
+ |
" [%lf\t%lf\t%lf]\n" |
| 258 |
+ |
" [%lf\t%lf\t%lf]\n", |
| 259 |
+ |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 260 |
+ |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 261 |
+ |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 262 |
+ |
painCave.isFatal = 1; |
| 263 |
+ |
simError(); |
| 264 |
+ |
} else if (offDiagMax > 0.1) { |
| 265 |
+ |
sprintf( painCave.errMsg, |
| 266 |
+ |
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
| 267 |
+ |
" Check your tauBarostat, as it is probably too small!\n\n" |
| 268 |
+ |
" scaleMat = [%lf\t%lf\t%lf]\n" |
| 269 |
+ |
" [%lf\t%lf\t%lf]\n" |
| 270 |
+ |
" [%lf\t%lf\t%lf]\n", |
| 271 |
+ |
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
| 272 |
+ |
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
| 273 |
+ |
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
| 274 |
+ |
painCave.isFatal = 1; |
| 275 |
+ |
simError(); |
| 276 |
+ |
} else { |
| 277 |
+ |
info->getBoxM(hm); |
| 278 |
+ |
info->matMul3(hm, scaleMat, hmnew); |
| 279 |
+ |
info->setBoxM(hmnew); |
| 280 |
+ |
} |
| 281 |
+ |
|
| 282 |
|
} |
| 283 |
|
|
| 284 |
< |
void NPTi::moveB( void ){ |
| 285 |
< |
int i,j,k; |
| 286 |
< |
int atomIndex; |
| 284 |
> |
template<typename T> void NPTf<T>::moveB( void ){ |
| 285 |
> |
|
| 286 |
> |
//new version of NPTf |
| 287 |
> |
int i, j, k; |
| 288 |
|
DirectionalAtom* dAtom; |
| 289 |
< |
double Tb[3]; |
| 290 |
< |
double ji[3]; |
| 289 |
> |
double Tb[3], ji[3]; |
| 290 |
> |
double vel[3], myVel[3], frc[3]; |
| 291 |
> |
double mass; |
| 292 |
> |
|
| 293 |
|
double instaTemp, instaPress, instaVol; |
| 294 |
|
double tt2, tb2; |
| 295 |
+ |
double sc[3]; |
| 296 |
+ |
double press[3][3], vScale[3][3]; |
| 297 |
+ |
double oldChi, prevChi; |
| 298 |
+ |
double oldEta[3][3], prevEta[3][3], diffEta; |
| 299 |
|
|
| 300 |
|
tt2 = tauThermostat * tauThermostat; |
| 301 |
|
tb2 = tauBarostat * tauBarostat; |
| 302 |
|
|
| 303 |
< |
instaTemp = tStats->getTemperature(); |
| 193 |
< |
instaPress = tStats->getPressure(); |
| 194 |
< |
instaVol = tStats->getVolume(); |
| 303 |
> |
// Set things up for the iteration: |
| 304 |
|
|
| 305 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 197 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
| 305 |
> |
oldChi = chi; |
| 306 |
|
|
| 307 |
+ |
for(i = 0; i < 3; i++) |
| 308 |
+ |
for(j = 0; j < 3; j++) |
| 309 |
+ |
oldEta[i][j] = eta[i][j]; |
| 310 |
+ |
|
| 311 |
|
for( i=0; i<nAtoms; i++ ){ |
| 312 |
< |
atomIndex = i * 3; |
| 312 |
> |
|
| 313 |
> |
atoms[i]->getVel( vel ); |
| 314 |
> |
|
| 315 |
> |
for (j=0; j < 3; j++) |
| 316 |
> |
oldVel[3*i + j] = vel[j]; |
| 317 |
> |
|
| 318 |
> |
if( atoms[i]->isDirectional() ){ |
| 319 |
> |
|
| 320 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
| 321 |
> |
|
| 322 |
> |
dAtom->getJ( ji ); |
| 323 |
> |
|
| 324 |
> |
for (j=0; j < 3; j++) |
| 325 |
> |
oldJi[3*i + j] = ji[j]; |
| 326 |
> |
|
| 327 |
> |
} |
| 328 |
> |
} |
| 329 |
> |
|
| 330 |
> |
// do the iteration: |
| 331 |
> |
|
| 332 |
> |
instaVol = tStats->getVolume(); |
| 333 |
> |
|
| 334 |
> |
for (k=0; k < 4; k++) { |
| 335 |
|
|
| 336 |
< |
// velocity half step |
| 337 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 338 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
| 339 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
| 340 |
< |
- vel[j]*(chi+eta)); |
| 336 |
> |
instaTemp = tStats->getTemperature(); |
| 337 |
> |
tStats->getPressureTensor(press); |
| 338 |
> |
|
| 339 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
| 340 |
> |
|
| 341 |
> |
prevChi = chi; |
| 342 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
| 343 |
|
|
| 344 |
< |
if( atoms[i]->isDirectional() ){ |
| 344 |
> |
for(i = 0; i < 3; i++) |
| 345 |
> |
for(j = 0; j < 3; j++) |
| 346 |
> |
prevEta[i][j] = eta[i][j]; |
| 347 |
> |
|
| 348 |
> |
//advance eta half step and calculate scale factor for velocity |
| 349 |
> |
|
| 350 |
> |
for(i = 0; i < 3; i ++) |
| 351 |
> |
for(j = 0; j < 3; j++){ |
| 352 |
> |
if( i == j) { |
| 353 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
| 354 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
| 355 |
> |
vScale[i][j] = eta[i][j] + chi; |
| 356 |
> |
} else { |
| 357 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
| 358 |
> |
vScale[i][j] = eta[i][j]; |
| 359 |
> |
} |
| 360 |
> |
} |
| 361 |
> |
|
| 362 |
> |
for( i=0; i<nAtoms; i++ ){ |
| 363 |
> |
|
| 364 |
> |
atoms[i]->getFrc( frc ); |
| 365 |
> |
atoms[i]->getVel(vel); |
| 366 |
|
|
| 367 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
| 367 |
> |
mass = atoms[i]->getMass(); |
| 368 |
> |
|
| 369 |
> |
for (j = 0; j < 3; j++) |
| 370 |
> |
myVel[j] = oldVel[3*i + j]; |
| 371 |
|
|
| 372 |
< |
// get and convert the torque to body frame |
| 372 |
> |
info->matVecMul3( vScale, myVel, sc ); |
| 373 |
|
|
| 374 |
< |
Tb[0] = dAtom->getTx(); |
| 375 |
< |
Tb[1] = dAtom->getTy(); |
| 376 |
< |
Tb[2] = dAtom->getTz(); |
| 374 |
> |
// velocity half step |
| 375 |
> |
for (j=0; j < 3; j++) { |
| 376 |
> |
// velocity half step (use chi from previous step here): |
| 377 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
| 378 |
> |
} |
| 379 |
|
|
| 380 |
< |
dAtom->lab2Body( Tb ); |
| 380 |
> |
atoms[i]->setVel( vel ); |
| 381 |
|
|
| 382 |
< |
// get the angular momentum, and complete the angular momentum |
| 383 |
< |
// half step |
| 382 |
> |
if( atoms[i]->isDirectional() ){ |
| 383 |
> |
|
| 384 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
| 385 |
> |
|
| 386 |
> |
// get and convert the torque to body frame |
| 387 |
> |
|
| 388 |
> |
dAtom->getTrq( Tb ); |
| 389 |
> |
dAtom->lab2Body( Tb ); |
| 390 |
> |
|
| 391 |
> |
for (j=0; j < 3; j++) |
| 392 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 393 |
|
|
| 394 |
< |
ji[0] = dAtom->getJx(); |
| 395 |
< |
ji[1] = dAtom->getJy(); |
| 225 |
< |
ji[2] = dAtom->getJz(); |
| 226 |
< |
|
| 227 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 228 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 229 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 230 |
< |
|
| 231 |
< |
dAtom->setJx( ji[0] ); |
| 232 |
< |
dAtom->setJy( ji[1] ); |
| 233 |
< |
dAtom->setJz( ji[2] ); |
| 394 |
> |
dAtom->setJ( ji ); |
| 395 |
> |
} |
| 396 |
|
} |
| 397 |
+ |
|
| 398 |
+ |
if (nConstrained) { |
| 399 |
+ |
constrainB(); |
| 400 |
+ |
} |
| 401 |
+ |
|
| 402 |
+ |
diffEta = 0; |
| 403 |
+ |
for(i = 0; i < 3; i++) |
| 404 |
+ |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
| 405 |
+ |
|
| 406 |
+ |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
| 407 |
+ |
break; |
| 408 |
|
} |
| 409 |
+ |
|
| 410 |
+ |
//calculate integral of chidt |
| 411 |
+ |
integralOfChidt += dt2*chi; |
| 412 |
+ |
|
| 413 |
|
} |
| 414 |
|
|
| 415 |
< |
int NPTi::readyCheck() { |
| 415 |
> |
template<typename T> void NPTf<T>::resetIntegrator() { |
| 416 |
> |
int i,j; |
| 417 |
> |
|
| 418 |
> |
chi = 0.0; |
| 419 |
> |
|
| 420 |
> |
for(i = 0; i < 3; i++) |
| 421 |
> |
for (j = 0; j < 3; j++) |
| 422 |
> |
eta[i][j] = 0.0; |
| 423 |
> |
|
| 424 |
> |
} |
| 425 |
> |
|
| 426 |
> |
template<typename T> int NPTf<T>::readyCheck() { |
| 427 |
> |
|
| 428 |
> |
//check parent's readyCheck() first |
| 429 |
> |
if (T::readyCheck() == -1) |
| 430 |
> |
return -1; |
| 431 |
|
|
| 432 |
|
// First check to see if we have a target temperature. |
| 433 |
|
// Not having one is fatal. |
| 434 |
|
|
| 435 |
|
if (!have_target_temp) { |
| 436 |
|
sprintf( painCave.errMsg, |
| 437 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 437 |
> |
"NPTf error: You can't use the NPTf integrator\n" |
| 438 |
|
" without a targetTemp!\n" |
| 439 |
|
); |
| 440 |
|
painCave.isFatal = 1; |
| 444 |
|
|
| 445 |
|
if (!have_target_pressure) { |
| 446 |
|
sprintf( painCave.errMsg, |
| 447 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 447 |
> |
"NPTf error: You can't use the NPTf integrator\n" |
| 448 |
|
" without a targetPressure!\n" |
| 449 |
|
); |
| 450 |
|
painCave.isFatal = 1; |
| 456 |
|
|
| 457 |
|
if (!have_tau_thermostat) { |
| 458 |
|
sprintf( painCave.errMsg, |
| 459 |
< |
"NPTi error: If you use the NPTi\n" |
| 459 |
> |
"NPTf error: If you use the NPTf\n" |
| 460 |
|
" integrator, you must set tauThermostat.\n"); |
| 461 |
|
painCave.isFatal = 1; |
| 462 |
|
simError(); |
| 467 |
|
|
| 468 |
|
if (!have_tau_barostat) { |
| 469 |
|
sprintf( painCave.errMsg, |
| 470 |
< |
"NPTi error: If you use the NPTi\n" |
| 470 |
> |
"NPTf error: If you use the NPTf\n" |
| 471 |
|
" integrator, you must set tauBarostat.\n"); |
| 472 |
|
painCave.isFatal = 1; |
| 473 |
|
simError(); |
| 474 |
|
return -1; |
| 475 |
|
} |
| 476 |
|
|
| 477 |
< |
// We need NkBT a lot, so just set it here: |
| 477 |
> |
|
| 478 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
| 479 |
> |
// of particles, so no subtraction or addition of constraints or |
| 480 |
> |
// orientational degrees of freedom: |
| 481 |
> |
|
| 482 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
| 483 |
> |
|
| 484 |
> |
// fkBT is used because the thermostat operates on more degrees of freedom |
| 485 |
> |
// than the barostat (when there are particles with orientational degrees |
| 486 |
> |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
| 487 |
> |
|
| 488 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
| 489 |
|
|
| 287 |
– |
NkBT = (double)info->ndf * kB * targetTemp; |
| 288 |
– |
|
| 490 |
|
return 1; |
| 491 |
|
} |
| 492 |
+ |
|
| 493 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
| 494 |
+ |
|
| 495 |
+ |
double conservedQuantity; |
| 496 |
+ |
double Energy; |
| 497 |
+ |
double thermostat_kinetic; |
| 498 |
+ |
double thermostat_potential; |
| 499 |
+ |
double barostat_kinetic; |
| 500 |
+ |
double barostat_potential; |
| 501 |
+ |
double trEta; |
| 502 |
+ |
double a[3][3], b[3][3]; |
| 503 |
+ |
|
| 504 |
+ |
Energy = tStats->getTotalE(); |
| 505 |
+ |
|
| 506 |
+ |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 507 |
+ |
(2.0 * eConvert); |
| 508 |
+ |
|
| 509 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 510 |
+ |
|
| 511 |
+ |
info->transposeMat3(eta, a); |
| 512 |
+ |
info->matMul3(a, eta, b); |
| 513 |
+ |
trEta = info->matTrace3(b); |
| 514 |
+ |
|
| 515 |
+ |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
| 516 |
+ |
(2.0 * eConvert); |
| 517 |
+ |
|
| 518 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 519 |
+ |
eConvert; |
| 520 |
+ |
|
| 521 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 522 |
+ |
barostat_kinetic + barostat_potential; |
| 523 |
+ |
|
| 524 |
+ |
cout.width(8); |
| 525 |
+ |
cout.precision(8); |
| 526 |
+ |
|
| 527 |
+ |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 528 |
+ |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 529 |
+ |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 530 |
+ |
|
| 531 |
+ |
return conservedQuantity; |
| 532 |
+ |
} |
